biointerchange 1.0.1 → 1.0.2

data/web/bootstrap/js/bootstrap.min.js

@@ -1,6 +1,6 @@
 /*!
-* Bootstrap.js by @fat & @mdo
-* Copyright 2012 Twitter, Inc.
-* http://www.apache.org/licenses/LICENSE-2.0.txt
-*/
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data/web/cli.html

@@ -9,14 +9,13 @@
 
     <!-- Le styles -->
     <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
+    <link href="bootstrap/css/bootstrapi-theme.min.css" rel="stylesheet">
     <style type="text/css">
       body {
         padding-top: 60px;
         padding-bottom: 40px;
       }
     </style>
-    <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
-    <script src="bootstrap/js/jquery-1.8.1.min.js"></script>
 
     <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
     <!--[if lt IE 9]>
@@ -29,26 +28,22 @@
 
   <body>
     <a href="https://github.com/BioInterchange/BioInterchange"><img style="z-index: 5000; position: fixed; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png" alt="Fork me on GitHub"></a>
+
     <div class="navbar navbar-inverse navbar-fixed-top">
-      <div class="navbar-inner">
-        <div class="container">
-          <a class="brand" href="index.html">BioInterchange</a>
-          <ul class="nav">
-            <li class="active"><a href="cli.html">Shell Tool</a></li>
-            <li><a href="webservices.html">Web-Services</a></li>
-            <li><a href="api.html">API</a></li>
-            <li><a href="ontologies.html">Ontologies</a></li>
-            <li><a href="about.html">About</a></li>
-          </ul>
-        </div>
+      <div class="container-fluid">
+        <a class="navbar-brand" href="index.html">BioInterchange</a>
+        <ul class="nav navbar-nav">
+          <li class="active"><a href="cli.html">Shell Tool</a></li>
+          <li><a href="ontologies.html">Ontologies</a></li>
+          <li><a href="about.html">About</a></li>
+        </ul>
       </div>
     </div>
-
     <div class="container">
 
       <!-- Example row of columns -->
       <div class="row">
-        <div class="span12">
+        <div class="col-md-12">
           <h1>Shell Tool</h1>
           <p>
             BioInterchange's command-line tool <code>biointerchange</code> can be installed as a command line tools as follows:
@@ -60,7 +55,7 @@ gem install biointerchange
           <p>
             Examples:
 <pre>
-biointerchange --input biointerchange.gvf --rdf rdf.biointerchange.gvf --batchsize 100 --file examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
+biointerchange --input biointerchange.gvf --rdf rdf.biointerchange.gfvo --batchsize 100 --file examples/estd176_Banerjee_et_al_2011.2012-11-29.NCBI36.gvf
 biointerchange --input dbcls.catanns.json --rdf rdf.bh12.sio --file examples/pubannotation.10096561.json --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
 biointerchange --input uk.ac.man.pdfx --rdf rdf.bh12.sio --file examples/gb-2007-8-3-R40.xml --annotate_name 'Peter Smith' --annotate_name_id 'peter.smith@example.com'
 biointerchange --input phylotastic.newick --rdf rdf.phylotastic.newick --file examples/tree2.new --annotate_date '1 June 2006'
@@ -75,8 +70,8 @@ biointerchange --input phylotastic.newick --rdf rdf.phylotastic.newick --file ex
             </ul>
             Output formats:
             <ul>
-              <li><code>rdf.biointerchange.gff3</code>: RDFization of <code>biointerchange.gff3</code></li>
-              <li><code>rdf.biointerchange.gvf</code>: RDFization of <code>biointerchange.gvf</code></li>
+              <li><code>rdf.biointerchange.gfvo</code>: RDFization of <code>biointerchange.gff3</code></li>
+              <li><code>rdf.biointerchange.gfvo</code>: RDFization of <code>biointerchange.gvf</code></li>
               <li><code>rdf.bh12.sio</code>: RDFization of <code>dbcls.catanns.json</code> or <code>uk.ac.man.pdfx</code></li>
               <li><code>rdf.phylotastic.newick</code>: RDFization of <code>phylotastic.newick</code></li>
             </ul>
@@ -101,15 +96,6 @@ testrepo&gt; sparql select * where { ?s ?p ?o } .
 testrepo&gt; sparql select * where { ?s &lt;http://www.biointerchange.org/gvf1o#GVF1_0004&gt; ?o } .
 </pre>
           </p>
-          <h4>Data Consistency Verification</h4>
-          <p>
-            Data consistency is verifyable for the output formats <code>rdf.biointerchange.gff3</code> and <code>rdf.biointerchange.gvf</code> using the BioInterchange <a href="ontologies.html">ontologies</a> GFF3O and GVF1O. The following is an example of how <a href="http://jena.apache.org">Jena</a>'s command line tools and the <a href="http://hermit-reasoner.com">HermiT reasoner</a> can be used for conistency verification:
-<pre>
-rdfcat &lt;path-to-gff3o/gvf1o&gt; &lt;yourdata.n3&gt; &gt; merged.xml
-java -d64 -Xmx4G -jar HermiT.jar -k -v merged.xml
-</pre>
-            Another approach is to load the data and its related GFF3O/GVF1O ontology into <a href="http://protege.stanford.edu">Protege</a>, merge them, and then use the "Explain inconsistent ontology" menu item to inspect possible data inconsistencies.
-          </p>
           <h4>Example Data Provenance</h4>
           <p>
             The following list provides information on the origin of the example-data files in the <code>examples</code> directory:
@@ -128,7 +114,7 @@ java -d64 -Xmx4G -jar HermiT.jar -k -v merged.xml
       <hr>
 
       <footer>
-        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2014</p>
       </footer>
 
     </div> <!-- /container -->

data/web/index.html

@@ -9,13 +9,13 @@
 
     <!-- Le styles -->
     <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
+    <link href="bootstrap/css/bootstrap-theme.min.css" rel="stylesheet">
     <style type="text/css">
       body {
         padding-top: 60px;
         padding-bottom: 40px;
       }
     </style>
-    <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
 
     <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
     <!--[if lt IE 9]>
@@ -28,27 +28,24 @@
 
   <body>
     <a href="https://github.com/BioInterchange/BioInterchange"><img style="z-index: 5000; position: fixed; top: 0; right: 0; border: 0;" src="https://s3.amazonaws.com/github/ribbons/forkme_right_gray_6d6d6d.png" alt="Fork me on GitHub"></a>
+
     <div class="navbar navbar-inverse navbar-fixed-top">
-      <div class="navbar-inner">
-        <div class="container">
-          <a class="brand" href="index.html">BioInterchange</a>
-          <ul class="nav">
-            <li><a href="cli.html">Shell Tool</a></li>
-            <li><a href="webservices.html">Web-Services</a></li>
-            <li><a href="api.html">API</a></li>
-            <li><a href="ontologies.html">Ontologies</a></li>
-            <li><a href="about.html">About</a></li>
-          </ul>
-        </div>
+      <div class="container-fluid">
+        <a class="navbar-brand" href="index.html">BioInterchange</a>
+        <ul class="nav navbar-nav">
+          <li><a href="cli.html">Shell Tool</a></li>
+          <li><a href="ontologies.html">Ontologies</a></li>
+          <li><a href="about.html">About</a></li>
+        </ul>
       </div>
     </div>
 
     <div class="container">
 
-      <div class="hero-unit">
-        <div style="float: left; margin-right: 24px;"><a href="http://www.biointerchange.org"><img width=150 height=150 src="images/BioInterchange300.png" /></a></div>
+      <div style="margin-top: 32px;" class="jumbotron">
+        <div style="float: left; margin-right: 24px; margin-top: 48px;"><a href="http://www.biointerchange.org"><img width=150 height=150 src="images/BioInterchange300.png" /></a></div>
         <h1>BioInterchange</h1>
-        <p>Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF, Newick and other files. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API.<div class="alert alert-info" style="text-align: center;"><a class="icon-warning-sign"></a><i>&nbsp;We are currently moving over to <a href="ontologies.html" style="font-weight: bold;">GFVO</a> for converting GFF3, GTF, GVF and VCF files to RDF.</i></div></p>
+        <p>Interchange data using the Resource Description Framework (RDF) and let BioInterchange automagically create RDF triples from your TSV, XML, GFF3, GVF, VCF, Newick and other files. BioInterchange helps you transform your data sets into linked data for sharing and data integration via command line, web-service, or API.</p>
         <!-- <p><a class="btn btn-primary btn-large">Learn more &raquo;</a></p> -->
         <div style="float: right;">
           <a href="https://twitter.com/BioInterchange" class="twitter-follow-button" data-show-count="false" data-size="large">Follow @BioInterchange</a>
@@ -57,28 +54,13 @@
       </div>
 
       <div class="row">
-        <div class="span6" style="text-align: justify;">
+        <div class="col-md-6" style="text-align: justify;">
           <h2>Shell Tool</h2>
           <p>Create RDF files from large data sets using the BioInterchange shell tool. It is installed as a Ruby gem that works with Mac OS X, Linux and Windows.</p>
           <p>Check out how the shell tool turns data into RDF using a single command line call, how the data can be loaded into a triple store, and how to use a semantic reasoner to verify your data consistency!</p>
           <p><a class="btn" href="cli.html">View details &raquo;</a></p>
         </div>
-        <div class="span6" style="text-align: justify;">
-          <h2>Web-Services</h2>
-          <p>Quickly RDFize small data snippets with BioInterchange's web-service. Either copy/paste your data into an interactive web-site, or use the RESTful web-service.</p>
-          <p>Example data is provided for every input format that BioInterchange can turn into RDF. Turn it into RDF with a click of a button!</p>
-          <p><a class="btn" href="webservices.html">View details &raquo;</a></em></p>
-       </div>
-      </div>
-      <div class="row">
-        <div class="span6" style="text-align: justify;">
-          <h2>API</h2>
-          <p>Integrate BioInterchange into your Ruby programs as a gem. The small footprint API makes it possible to create RDF from simple data structures in a few lines.</p>
-          <p>See how the BioInterchange API framework can be used with Ruby, Python and Java; learn how to implement your own RDF transformation algorithms!</p>
-          <p><a class="btn" href="api.html">View details &raquo;</a></p>
-          <p><a class="btn" href="../doc/BioInterchange.html">View Ruby docs &raquo;</a></p>
-        </div>
-        <div class="span6" style="text-align: justify;">
+        <div class="col-md-6" style="text-align: justify;">
           <h2>Ontologies</h2>
           <p>Reuse ontologies that we specifically developed to tackle some RDFizations. External ontologies that are used by BioInterchange are listed here too.</p>
           <p>Incorporate the ontologies into your own projects and get easy programmatic access to them using the BioInterchange vocabulary wrappers!</p>
@@ -89,7 +71,7 @@
       <hr>
 
       <footer>
-        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2014</p>
       </footer>
 
     </div> <!-- /container -->

data/web/ontologies.html

@@ -8,21 +8,15 @@
     <meta name="author" content="Joachim Baran">
 
     <!-- Le styles -->
-    <link href="bootstrap/css/bootstrap.css" rel="stylesheet">
+    <link href="bootstrap/css/bootstrap.min.css" rel="stylesheet">
+    <link href="bootstrap/css/bootstrapi-theme.min.css" rel="stylesheet">
     <style type="text/css">
       body {
         padding-top: 60px;
         padding-bottom: 40px;
       }
     </style>
-    <link href="bootstrap/css/bootstrap-responsive.css" rel="stylesheet">
-
-    <script type="text/javascript">
-    // Magic Sauce. See https://github.com/twitter/bootstrap/issues/1768
-      var shiftWindow = function() { scrollBy(0, -50) };
-      if (location.hash) shiftWindow();
-      window.addEventListener("hashchange", shiftWindow);
-    </script>
+
     <!-- Le HTML5 shim, for IE6-8 support of HTML5 elements -->
     <!--[if lt IE 9]>
       <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
@@ -35,17 +29,13 @@
   <body>
 
     <div class="navbar navbar-inverse navbar-fixed-top">
-      <div class="navbar-inner">
-        <div class="container">
-          <a class="brand" href="index.html">BioInterchange</a>
-          <ul class="nav">
-            <li><a href="cli.html">Shell Tool</a></li>
-            <li><a href="webservices.html">Web-Services</a></li>
-            <li><a href="api.html">API</a></li>
-            <li class="active"><a href="ontologies.html">Ontologies</a></li>
-            <li><a href="about.html">About</a></li>
-          </ul>
-        </div>
+      <div class="container-fluid">
+        <a class="navbar-brand" href="index.html">BioInterchange</a>
+        <ul class="nav navbar-nav">
+          <li><a href="cli.html">Shell Tool</a></li>
+          <li class="active"><a href="ontologies.html">Ontologies</a></li>
+          <li><a href="about.html">About</a></li>
+        </ul>
       </div>
     </div>
 
@@ -53,7 +43,7 @@
 
       <!-- Example row of columns -->
       <div class="row">
-        <div class="span12">
+        <div class="col-md-12">
           <h2>Overview</h2>
           <p>BioInterchange makes use of several external ontologies, i.e. ontologies that were developed outside the scope of the BioInterchange project. We are always happy to hear about ontologies that we should consider incorporating into BioInterchange and we welcome contributions of ontologies that permit including more file formats for RDF conversion.</p>
           <p>External ontologies used in BioInterchange:
@@ -73,30 +63,82 @@
             <li><a href="#external">External Ontologies and Linked Data</a></li>
             <li><a href="#examples">Examples</a></li>
             <ol style="list-style-type: lower-alpha;">
-              <li><a href="#example1">Example 1: Loci and Basic Genomic Feature Annotations</a></li>
-              <li><a href="#example1">Example 2: Encoding of a Sequence Alignment</a></li>
+              <li><a href="#example1">Example 1: Loci and Basic Genomic Feature Annotation of a Gene and its Transcription Factor Binding Site</a></li>
+              <li><a href="#example2">Example 2: Encoding of a Sequence Alignment</a></li>
+              <li><a href="#example3">Example 3: Phased and Unphased Genotype and its Sequence Variants</a></li>
+              <li><a href="#example4">Example 4: Encoding of a Phred Score</a></li>
             </ol>
           </ol>
-          <div class="alert alert-info"><p><b>Note: </b> <span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span>and <span style="margin-right: 4px;" class="badge badge-warning">VCF</span> badges indicate a particular class or property definition's origin. The application of the class or property is not restricted to those file formats though.</p></div>
-          <p>GFVO is being developed as the joint work of <a href="http://joachimbaran.wordpress.com">Joachim Baran</a> (<i>corresponding author</i>, <i>joachim.baran</i><b>&#64;</b><i>gmail.com</i>), <a href="http://utah.academia.edu/BDurgahee">Begum Durgahee</a>, <a href="http://medicine.utah.edu/faculty/mddetail.php?facultyID=u0514925">Karen Eilbeck</a>, <a href="http://ntnu-no.academia.edu/ErickAntezana">Erick Antezana</a>, <a href="http://leechuck.de">Robert Hoehndorf</a>, and <a href="http://dumontierlab.com">Michel Dumontier</a>.</p>
-          <p>Feedback on the ontology has been provided by <a href="http://www.linkedin.com/in/raoulbonnal">Raoul Bonnal</a>, <a href="http://www.linkedin.com/in/francescostrozzi">Francesco Strozzi</a>, and <a href="http://www.linkedin.com/in/toshiakikatayama">Toshiaki Katayama</a>.</p>
+          <div class="alert"><p><b>Note: </b> <span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span>and <span style="margin-right: 4px;" class="badge alert-warning">VCF</span> badges indicate a particular class or property definition's origin. The application of the ontology is not restricted to those file formats though.</p></div>
+          <p>GFVO is being developed as the joint work of <a href="http://joachimbaran.wordpress.com">Joachim Baran</a> (<i>corresponding author</i>, <i>joachim.baran</i><b>&#64;</b><i>gmail.com</i>), <a href="http://ntnu-no.academia.edu/ErickAntezana">Erick Antezana</a>, <a href="http://www.linkedin.com/in/raoulbonnal">Raoul Bonnal</a>, <a href="http://utah.academia.edu/BDurgahee">Begum Durgahee</a>, <a href="http://medicine.utah.edu/faculty/mddetail.php?facultyID=u0514925">Karen Eilbeck</a>, <a href="http://leechuck.de">Robert Hoehndorf</a>, <a href="http://www.linkedin.com/in/toshiakikatayama">Toshiaki Katayama</a>, <a href="http://www.linkedin.com/in/francescostrozzi">Francesco Strozzi</a>, <a href="https://www.linkedin.com/in/takatomofujisawa">Takatomo Fujisawa</a>, and <a href="http://dumontierlab.com">Michel Dumontier</a>.</p>
+          <p>Feedback on the ontology has been provided by <a href="http://berkeleybop.org/person/chris-mungall">Chris Mungall</a>.</p>
+          <h3 id="bioportal">Overview</h3>
+          <p>An overview of GFVO is available through its <a href="http://bioportal.bioontology.org/ontologies/GFVO/?p=classes&amp;conceptid=root">BioPortal web-page</a>.
+          <div class="alert alert-info" style="text-align: center;"><a class="icon-warning-sign"></a><i>&nbsp;Due to technical limitations of BioPortal, GFVO in BioPortal does not import other ontologies nor does it contain SIO class- or property-equivalences.</i><br><br><i>It is necessary to use <a href="http://protege.stanford.edu/">Protege</a> or <a href="http://www.topquadrant.com/tools/ide-topbraid-composer-maestro-edition/">TopBraid Composer</a> for viewing the ontology properly (e.g., to see GFF3/GTF/GVF/VCF specification annotations, Wikipedia linkouts, class-/property-equivalences, etc.).</i><br><br><i>The BioPortal GFVO version is available at: <a href="http://www.biointerchange.org/gfvo_bioportal">http://www.biointerchange.org/gfvo_bioportal</a></i></div>
+          </p>
+          <object type="text/html" data="http://bioportal.bioontology.org/ontologies/GFVO/?p=classes&amp;conceptid=root" width="1200px" height="900px" style="overflow:auto;border:1px solid #333333"></object>
+          <h3 id="bestpractices">Best Practices</h3>
+          <p>The ontology design adheres to the following best practices:
+            <ol>
+              <li>The class hierarchy, object- and datatype-property hierarchies are modeled to match <a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO) hierarchies.</li>
+              <li>Every class and property has a label (rdfs:label) as well as a description (rdfs:comment). The description may contain an example of how a class/property is being applied.</li>
+              <li>Classes that are directly related to either GFF3, GTF, GVF or VCF specification have a link-out to the specification&apos;s document as provenance indicator (via rdfs:isDefinedBy).</li>
+              <li>Link-outs to Wikipedia are provided for classes whereever possible.</li>
+              <li>Ontology terms are encoded in the URIs using camel case, i.e. letters following a white space in an ontology term are capitalized followed by the removal of the white space.</li>
+            </ol>
+          </p>
           <h3 id="external">External Ontologies and Linked Data</h3>
-          <p>GFVO makes use of the <a href="https://github.com/JervenBolleman/FALDO">Feature Annotation Location Description Ontology</a> (<a href="https://github.com/JervenBolleman/FALDO">FALDO</a>) for describing genomic locations such as genomic features, breakpoints, and coordinate ranges for fuzzy/probabilistic coordinate ranges. We also integrate the <a href="http://variationontology.org">Variation Ontology</a> (<a href="http://variationontology.org">VariO</a>) for describing variants, their effects and conseuences.</p>
+          <p>GFVO makes use of the <a href="http://www.sequenceontology.org">Sequence Ontology</a> for annotating genomic features and variants as well as the <a href="https://github.com/JervenBolleman/FALDO">Feature Annotation Location Description Ontology</a> (<a href="https://github.com/JervenBolleman/FALDO">FALDO</a>) for describing genomic locations such as genomic features, breakpoints, and coordinate ranges for fuzzy/probabilistic coordinate ranges. We also integrate the <a href="http://variationontology.org">Variation Ontology</a> (<a href="http://variationontology.org">VariO</a>) for describing variants, their effects and consequences.</p>
           <p>Species are represented as linked data by URIs to NCBI's <a href="http://www.ncbi.nlm.nih.gov/taxonomy">species taxonomy</a>. We encourage the use of <a href="http://identifiers.org">identifiers.org</a> URIs for other entities, which will be automatically be supported in the BioInterchange's RDF output with its next release.</p>
+          <p>The design patterns of GFVO follow the <a href="http://code.google.com/p/semanticscience/wiki/SIO">SIO</a> and equivalence mappings are provided for GFVO's classes, object- and datatype-properties where applicable.</p>
+          <h3>Statistics</h3>
+          <p>Summary statistics about the number of classes and properties of GFVO are provided in the following table. The breakdown of the classes based on their modeling origin does not sum up to the total number of classes, because some modeled classes appear in multiple specifications (e.g., "DNA Sequence" appears in all four specifications).</p>
+          <table class="table table-striped table-bordered" style="margin-left: 15px; margin-right: 15px;">
+          <thead>
+            <tr>
+              <th></th>
+              <th>Total Number</th>
+              <th>Number of Equivalences to SIO</th>
+            </tr>
+          </thead>
+          <tbody>
+<!-- Imported via :r!~/src/Ontologies/scripts/stats.rb < ~/src/Ontologies/gfvo.xml -->
+<tr><td>Classes</td><td>92</td><td>41</td></tr>
+<tr><td>&hellip;modeled from GFF3</td><td>27</td><td>15</td></tr>
+<tr><td>&hellip;modeled from GTF</td><td>17</td><td>13</td></tr>
+<tr><td>&hellip;modeled from GVF</td><td>56</td><td>24</td></tr>
+<tr><td>&hellip;modeled from VCF</td><td>25</td><td>16</td></tr>
+<tr><td>&hellip;with Wikipedia reference</td><td>48</td><td></td></tr>
+<tr><td>Datatype properties</td><td>1</td><td>1</td></tr>
+<tr><td>Object properties</td><td>32</td><td>31</td></tr>
+          </tbody>
+          </table>
+<!--
+          <h3 id="hierarchy">Hierarchy Overview</h3>
+          <div class="row">
+            <div class="col-md-4 text-center">
+              <img src="gfvo_classes.png" />
+              <p>Class hierarchy of GFVO (SIO equivalences omitted)</p>
+            </div>
+            <div class="col-md-4 text-center">
+              <p>TODO</p>
+              <p>Object property hierarchy of GFVO (SIO equivalences omitted)</p>
+            </div>
+            <div class="col-md-4 text-center">
+              <p>TODO</p>
+              <p>Datatype property hierarchy of GFVO (SIO equivalences omitted)</p>
+            </div>
+          </div>
+-->
           <h3 id="examples">Examples</h3>
-          <h4 id="example1">Example 1: Loci and Basic Genomic Feature Annotations</h4>
+          <p>Examples are provided in Turtle syntax. All examples are archived and downloadable as the file &quot;<a href="https://github.com/BioInterchange/Ontologies">gfvo_examples.ttl</a>&quot; of the ontologies' GitHub repository.</p>
+          <h4 id="example1">Example 1: Loci and Basic Genomic Feature Annotation of a Gene and its Transcription Factor Binding Site</h4>
           <p>Encoding loci and basic genomic feature annotations. The example covers lines 0-3 of the example gene description given in the <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3 specification</a>.</p>
 <pre style="font-size: 10px; line-height: 13px;">
 @prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
-@prefix dc: &lt;http://purl.org/dc/terms/&gt; .
-@prefix owl: &lt;http://www.w3.org/2002/07/owl#&gt; .
 @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
-@prefix xml: &lt;http://www.w3.org/XML/1998/namespace&gt; .
-@prefix xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; .
-@prefix rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .
 @prefix faldo: &lt;http://biohackathon.org/resource/faldo#&gt; .
-@prefix vario: &lt;http://purl.obolibrary.org/obo/&gt; .
-@base &lt;http://www.biointerchange.org/gfvo#&gt; .
+@prefix so: &lt;http://purl.bioontology.org/ontology/SO/SO&gt; .
 
 #################################################################
 #
@@ -112,81 +154,125 @@
 #    binary RDF encodings such as RDF/HDT permits a more concise
 #    representation of the same data.
 #
+#    This example also avoids blank nodes, so that this file can
+#    be conveniently viewed using the Protege ontology editor.
+#    Using blank nodes, the line
+#
+#        :hasIdentifier :ExampleSet1Feature1Identifier ;
+#
+#    can be substituted with
+#
+#        :hasIdentifier [
+#            a :Identifier ;
+#            :hasValue &quot;gene00001&quot; ;
+#        ]
+#
 #################################################################
 
-:ExampleSet1 rdf:type :File ,
-                      owl:NamedIndividual ;
-             :gffVersion "3" ;
-             rdfs:comment "A simple example of a hierarchical genomic feature dependency. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .
-
-:ExampleSet1ChromEnd rdf:type faldo:ExactPosition ,
-                              owl:NamedIndividual ;
-                     faldo:position "1497228" .
-
-:ExampleSet1ChromStart rdf:type faldo:ExactPosition ,
-                                owl:NamedIndividual ;
-                       faldo:position "1" .
-
-:ExampleSet1Feature1 rdf:type :Feature ,
-                              owl:NamedIndividual ;
-                     :id "gene00001" ;
-                     :name "EDEN" ;
-                     :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000704" ;
-                     :seqid :ExampleSet1Landmark1 .
-
-:ExampleSet1Feature1_2Start rdf:type faldo:ExactPosition ,
-                                     owl:NamedIndividual ;
-                            faldo:position "1000" .
-
-:ExampleSet1Feature2 rdf:type :Feature ,
-                              owl:NamedIndividual ;
-                     :id "tfbs00001" ;
-                     :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000235" ;
-                     :parent :ExampleSet1Feature1 ;
-                     :locus :ExampleSet1Region3 .
-
-:ExampleSet1Feature2End rdf:type faldo:ExactPosition ,
-                                 owl:NamedIndividual ;
-                        faldo:position "1012" .
-
-:ExampleSet1Landmark1 rdf:type :Landmark ,
-                               owl:NamedIndividual ;
-                      :id "ctg123" ;
-                      :locus :ExampleSet1Region1 .
-
-:ExampleSet1Region1 rdf:type faldo:Region ,
-                             owl:NamedIndividual ;
-                    faldo:begin :ExampleSet1ChromEnd ,
-                                :ExampleSet1ChromStart .
-
-:ExampleSet1Region2 rdf:type faldo:ForwardStrandPosition ,
-                             owl:NamedIndividual ;
-                    faldo:begin :ExampleSet1Feature1_2Start ;
-                    faldo:end :ExampleSet1Feature1End .
-
-:ExampleSet1Region3 rdf:type faldo:Region ,
-                             owl:NamedIndividual ;
-                    faldo:begin :ExampleSet1Feature1_2Start ;
-                    faldo:end :ExampleSet1Feature2End .
-
-:ExampleSet1Feature1End rdf:type faldo:ExactPosition ,
-                                owl:NamedIndividual ;
-                       faldo:position "9000" .
-</pre>
+# This example is representing the contents of a GFF3 file, version 3.
+:Example1Version a :Version ;
+                 :hasValue &quot;gff-version 3&quot; .
+
+# Two genomic features are described in the file, where an extra comment
+# was added to clarify the provenance of this example representation.
+:ExampleSet1 a :File ;
+             :hasIdentifier :Example1Version ;
+             :hasMember :ExampleSet1Feature1 ,
+                        :ExampleSet1Feature2 ;
+             rdfs:comment &quot;A simple example of a hierarchical genomic feature dependency. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html).&quot;@en .
+
+# Features in this example are placed on a single langmark, which has
+# an identifier associated with it (it cannot be anonymous in GFF3, even
+# though GFVO permits landmarks without explicit identifier), and it
+# has a range of sequence positions it covers (expressed by a separate
+# pragma statement in GFF3).
+:ExampleSet1Landmark a :Landmark ;
+                     :hasIdentifier :ExampleSet1LandmarkIdentifier ;
+                     :hasAttribute :ExampleSet1LandmarkRegion .
+
+:ExampleSet1LandmarkIdentifier a :Identifier ;
+                               :hasValue &quot;ctg123&quot; .
+
+:ExampleSet1LandmarkRegion a faldo:Region ;
+                           faldo:begin :ExampleSet1LandmarkStartPosition ;
+                           faldo:end :ExampleSet1LandmarkEndPosition .
+
+:ExampleSet1LandmarkStartPosition a faldo:ExactPosition ;
+                                  faldo:position &quot;1&quot; .
+
+:ExampleSet1LandmarkEndPosition a faldo:ExactPosition ;
+                                faldo:position &quot;1497228&quot; .
+
+# GFF3, GTF and GVF make use of named attributes. There are predefined (reserved)
+# names, but users can also freely contribute their own attributes. In this example,
+# only one labeled attribute is used, whose name we define upfront.
+#
+# Note: It might be a bit confusing that the label "Name" is applied to an attribute
+#       of type "Name". This is just an artifact of the chosen example and it is of
+#       course possible to label a "Name" attribute arbitrarily.
+:ExampleSet1AttributeName a :Label ;
+                          :hasValue &quot;Name&quot; .
+
+# First feature of the GFF3 file (line 2): a gene.
+:ExampleSet1Feature1 a :Feature ,
+                       so:0000704 ;
+                     :isLocatedOn :ExampleSet1Landmark ;
+                     :hasPart :ExampleSet1Feature1Locus ;
+                     :hasIdentifier :ExampleSet1Feature1Identifier ;
+                     :hasAttribute :ExampleSet1Feature1Name .
+
+:ExampleSet1Feature1Locus a :Locus ;
+                          :hasAttribute :ExampleSet1Feature1Region .
+
+:ExampleSet1Feature1Region a faldo:Region ;
+                           faldo:begin :ExampleSet1FeatureStartPosition ;
+                           faldo:end :ExampleSet1Feature1EndPosition .
+
+# The start coordinate of both features is the same in this example. So this
+# entity is used by both :ExampleSet1Feature1 and :ExampleSet1Feature2.
+:ExampleSet1FeatureStartPosition a faldo:ExactPosition ;
+                                 faldo:position &quot;1000&quot; .
+
+:ExampleSet1Feature1EndPosition a faldo:ExactPosition ;
+                                faldo:position &quot;9000&quot; .
+
+:ExampleSet1Feature1Identifier a :Identifier ;
+                               :hasValue &quot;gene00001&quot; .
+
+:ExampleSet1Feature1Name a :Name ;
+                         :hasAttribute :ExampleSet1AttributeName ;
+                         :hasValue &quot;EDEN&quot; .
+
+# Second feature of the GFF3 file (line 3): a transcription factor
+# binding site.
+# It references the first feature via a &quot;Parent&quot; attribute.
+:ExampleSet1Feature2 a :Feature ,
+                       so:0000235 ;
+                     :isLocatedOn :ExampleSet1Landmark ;
+                     :hasPart :ExampleSet1Feature2Locus ;
+                     :hasIdentifier :ExampleSet1Feature2Identifier ;
+                     :hasSource :ExampleSet1Feature1 .
+
+:ExampleSet1Feature2Locus a :Locus ;
+                          :hasAttribute :ExampleSet1Feature1Region .
+
+:ExampleSet1Feature2Region a faldo:Region ;
+                           faldo:begin :ExampleSet1FeatureStartPosition ;
+                           faldo:end :ExampleSet1Feature2EndPosition .
+
+:ExampleSet1Feature2EndPosition a faldo:ExactPosition ;
+                                faldo:position &quot;1012&quot; .
 
+:ExampleSet1Feature2Identifier a :Identifier ;
+                               :hasValue &quot;tfbs00001&quot; .
+</pre>
           <h4 id="example2">Example 2: Encoding of a Sequence Alignment</h4>
-          <p>Encoding of a sequence alignment. This is part of the <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3 specification</a>, denoting the alignment between the reference sequence "chr3" and the target sequence "EST23".</p>
+          <p>Encoding of a sequence alignment. This is part of the <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3 specification</a>, denoting the alignment between the reference sequence &quot;chr3&quot; and the target sequence &quot;EST23&quot;.</p>
 <pre style="font-size: 10px; line-height: 13px;">
 @prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
-@prefix dc: &lt;http://purl.org/dc/terms/&gt; .
-@prefix owl: &lt;http://www.w3.org/2002/07/owl#&gt; .
 @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
-@prefix xml: &lt;http://www.w3.org/XML/1998/namespace&gt; .
-@prefix xsd: &lt;http://www.w3.org/2001/XMLSchema#&gt; .
-@prefix rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .
 @prefix faldo: &lt;http://biohackathon.org/resource/faldo#&gt; .
-@prefix vario: &lt;http://purl.obolibrary.org/obo/&gt; .
-@base &lt;http://www.biointerchange.org/gfvo#&gt; .
+@prefix so: &lt;http://purl.bioontology.org/ontology/SO/SO&gt; .
 
 #################################################################
 #
@@ -194,1395 +280,1453 @@
 #
 #    Encoding of a sequence alignment. This is part of the GFF3
 #    specification, denoting the alignment between the reference
-#    sequence "chr3" and the target sequence "EST23".
+#    sequence &quot;chr3&quot; and the target sequence &quot;EST23&quot;.
 #           (http://www.sequenceontology.org/resources/gff3.html)
 #
 #################################################################
 
-:ExampleSet2 rdf:type :Set ,
-                      owl:NamedIndividual ;
-             rdfs:comment "An example of a sequence alignment. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html)."@en .
-
-:ExampleSet2Feature1 rdf:type :Feature ,
-                              owl:NamedIndividual ;
-                     :id "Match1" ;
-                     :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000343" ;
-                     :seqid :ExampleSet2Landmark1 .
-
-:ExampleSet2Feature2 rdf:type :Feature ,
-                              owl:NamedIndividual ;
-                     :id "EST23" ;
-                     :type "http://www.sequenceontology.org/browser/current_release/term/SO:0000345" ;
-                     :target :ExampleSet2Target1 .
-
-:ExampleSet2Landmark1 rdf:type :Landmark ,
-                               owl:NamedIndividual ;
-                      :id "chr3" .
-
-:ExampleSet2Target1 rdf:type :Target ,
-                             owl:NamedIndividual ;
-                    :alignment :ExampleSet2AlignmentOperation1 .
-
-:ExampleSet2AlignmentOperation1 rdf:type :AlignmentOperation ,
-                                owl:NamedIndividual ;
-                       :operation :Match ;
-                       :span "8" ;
-                       :first :ExampleSet2AlignmentOperation1 ;
-                       :rest :ExampleSet2AlignmentOperation2 .
-
-:ExampleSet2AlignmentOperation2 rdf:type :AlignmentOperation ,
-                                owl:NamedIndividual ;
-                       :operation :TargetSequenceGap ;
-                       :span "3" ;
-                       :first :ExampleSet2AlignmentOperation2 ;
-                       :rest :ExampleSet2AlignmentOperation3 .
-
-:ExampleSet2AlignmentOperation3 rdf:type :AlignmentOperation ,
-                                owl:NamedIndividual ;
-                       :operation :Match ;
-                       :span "6" ;
-                       :first :ExampleSet2AlignmentOperation3 ;
-                       :rest :ExampleSet2AlignmentOperation4 .
-
-:ExampleSet2AlignmentOperation4 rdf:type :AlignmentOperation ,
-                                owl:NamedIndividual ;
-                       :operation :ReferenceSequenceGap ;
-                       :span "1" ;
-                       :first :ExampleSet2AlignmentOperation4 ;
-                       :rest :ExampleSet2AlignmentOperation5 .
-
-:ExampleSet2AlignmentOperation5 rdf:type :AlignmentOperation ,
-                                owl:NamedIndividual ;
-                       :operation :Match ;
-                       :span "6" ;
-                       :first :ExampleSet2AlignmentOperation5 .
+:ExampleSet2 a :Collection ;
+             :hasMember :ExampleSet2Feature1 ,
+                        :ExampleSet2Feature2 ;
+             rdfs:comment &quot;An example of a sequence alignment. This example is an excerpt of another example given in the GFF3 specification (http://sequenceontology.org/resources/gff3.html).&quot;@en .
+
+:ExampleSet2Landmark a :Landmark ;
+                     :hasIdentifier :ExampleSet2LandmarkIdentifier .
+
+:ExampleSet2LandmarkIdentifier a :Identifier ;
+                               :hasValue &quot;chr3&quot; .
+
+# Reference sequence feature:
+:ExampleSet2Feature1 a :Feature ;
+                     :isLocatedOn :ExampleSet2Landmark ;
+                     :hasIdentifier :ExampleSet2Feature1Identifier .
+
+:ExampleSet1Feature1Identifier a :Identifier ;
+                               :hasValue &quot;Match1&quot; .
+
+# Target sequence feature:
+:ExampleSet2Feature2 a :Feature ;
+                       so:0000343 ;
+                     :isLocatedOn :ExampleSet2Landmark ;
+                     :hasIdentifier :ExampleSet2Feature2Identifier .
+
+:ExampleSet1Feature2Identifier a :Identifier ;
+                               :hasValue &quot;EST23&quot; .
+
+# Description of the sequence alignment between :ExampleSet2Feature1
+# and :ExampleSet2Feature2 (features &quot;Match1&quot; and &quot;EST23&quot;).
+:ExampleSet2SequenceAlignment a :SequenceAlignment ;
+                              :hasAttribute :ExampleSet2AlignmentLocus ;
+                              :hasSource :ExampleSet2Feature1 ;
+                              :hasInput :ExampleSet2Feature2 ;
+                              :hasFirstPart :ExampleSet2AlignmentOperation1 ;
+                              :hasOrderedPart :ExampleSet2AlignmentOperation2 ,
+                                              :ExampleSet2AlignmentOperation3 ,
+                                              :ExampleSet2AlignmentOperation4 ;
+                              :hasLastPart :ExampleSet2AlignmentOperation5 .
+
+# The locus describes the region over which the alignment operation
+# is being carried out.
+:ExampleSet2AlignmentLocus a :Locus ;
+                           :hasAttribute :ExampleSet2AlignmentRegion .
+
+:ExampleSet2AlignmentRegion a faldo:Region ;
+                            faldo:begin :ExampleSet2AlignmentStartPosition ;
+                            faldo:end :ExampleSet2AlignmentEndPosition .
+
+:ExampleSet2AlignmentStartPosition a faldo:ExactPosition ;
+                                   faldo:position &quot;1&quot; .
+
+:ExampleSet2AlignmentEndPosition a faldo:ExactPosition ;
+                                 faldo:position &quot;21&quot; .
+
+# Description of an actual alignment operation.
+:ExampleSet2AlignmentOperation1 rdf:type :Match ;
+                                :hasAttribute ::ExampleSet2AlignmentOperation1Span ;
+                                :isBefore :ExampleSet2AlignmentOperation2 .
+
+:ExampleSet2AlignmentOperation1Span a :Span ;
+                                    :hasValue &quot;8&quot; .
+
+:ExampleSet2AlignmentOperation2 rdf:type :TargetSequenceGap ;
+                                :hasAttribute ::ExampleSet2AlignmentOperation2Span ;
+                                :isAfter :ExampleSet2AlignmentOperation1 ;
+                                :isBefore :ExampleSet2AlignmentOperation3 .
+
+:ExampleSet2AlignmentOperation2Span a :Span ;
+                                    :hasValue &quot;3&quot; .
+
+:ExampleSet2AlignmentOperation3 rdf:type :Match ;
+                                :hasAttribute ::ExampleSet2AlignmentOperation3Span ;
+                                :isAfter :ExampleSet2AlignmentOperation2 ;
+                                :isBefore :ExampleSet2AlignmentOperation4 .
+
+:ExampleSet2AlignmentOperation3Span a :Span ;
+                                    :hasValue &quot;6&quot; .
+
+:ExampleSet2AlignmentOperation4 rdf:type :ReferenceSequenceGap ;
+                                :hasAttribute ::ExampleSet2AlignmentOperation4Span ;
+                                :isAfter :ExampleSet2AlignmentOperation3 ;
+                                :isBefore :ExampleSet2AlignmentOperation5 .
+
+:ExampleSet2AlignmentOperation4Span a :Span ;
+                                    :hasValue &quot;1&quot; .
+
+:ExampleSet2AlignmentOperation5 rdf:type :Match ;
+                                :hasAttribute ::ExampleSet2AlignmentOperation5Span ;
+                                :isAfter :ExampleSet2AlignmentOperation4 .
+
+:ExampleSet2AlignmentOperation5Span a :Span ;
+                                    :hasValue &quot;6&quot; .
+</pre>
+          <h4 id="example3">Example 3: Phased and Unphased Genotype and its Sequence Variants</h4>
+          <p>Encoding of a phased/unphased genotype and its sequence variants. This is part of the GVF specification, denoting two variants for two separate sequenced individuals: &quot;Variant_seq=A,T;Genotype=0:1,1:1&quot;. See &quot;Genotype&quot; in the <a href="http://www.sequenceontology.org/resources/gvf.html">GVF specification</a>.</p>
+<pre style="font-size: 10px; line-height: 13px;">
+@prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
+@prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
+
+#################################################################
+#
+#    Example 3
+#
+#    Encoding of genotypes/sequence variants. This is part of the GVF
+#    specification, denoting two variants for two separate
+#    sequenced individuals: &quot;Variant_seq=A,T;Genotype=0:1,1:1&quot;.
+#    (See &quot;Genotype&quot; in the GVF specification at
+#     http://www.sequenceontology.org/resources/gvf.html)
+#
+#################################################################
+
+:ExampleSet3 a :Collection ;
+             :hasMember :ExampleSet3Feature1 ;
+             rdfs:comment &quot;Encoding of genotypes/sequence variants. This example is part of the GVF specification, denoting two variants for two separate sequenced individuals (http://www.sequenceontology.org/resources/gvf.html).&quot;@en .
+
+# The individuals that were sequenced are represented by named, but otherwise
+# unspecified, instances. This provides sufficient information to distinguish
+# between the individuals that were sequenced.
+:ExampleSet3SequencedIndividual1 rdf:type :SequencedIndividual .
+:ExampleSet3SequencedIndividual2 rdf:type :SequencedIndividual .
+
+# Genomic feature that captures the two described genotypes.
+:ExampleSet3Feature1 a :Feature ;
+                     :hasAttribute :ExampleSet3Genotype1 ,
+                                   :ExampleSet3Genotype2 .
+
+# Genotype for the first individual.
+#
+# The genotype's phased variants are linked via &quot;hasFirstPart&quot; and
+# &quot;hasLastPart&quot; here, which are descendants of &qout;hasOrderedPart&quot;.
+# The object properties &quot;isBefore&quot;/&quot;isAfter&quot; connect the phased variants.
+#
+# Note: for an unphased genotype, it is sufficient to use &quot;hasPart&quot; only.
+:ExampleSet3Genotype1 a :Genotype ;
+                      :hasParticipant :ExampleSet3SequencedIndividual1 ;
+                      :hasQuality :Heterozygous ;
+                      :hasAttribute :ExampleSet3Phase ;
+                      :hasFirstPart :ExampleSet3ReferenceA_AT ;
+                      :hasLastPart :ExampleSet3VariantT_AT .
+
+# Ordering of the variants permits the expression of phased genotypes.
+# It is recommended to use &quot;isBefore&quot;, but the use of &quot;isAfter&quot; is optional.
+:ExampleSet3ReferenceA_AT :isBefore :ExampleSet3VariantT_AT .
+:ExampleSet3VariantT_AT :isAfter :ExampleSet3ReferenceA_AT .
+
+# Genotype of the second individual.
+:ExampleSet3Genotype2 a :Genotype ;
+                      :hasParticipant :ExampleSet3SequencedIndividual2 ;
+                      :hasQuality :Homozygous ;
+                      :hasAttribute :ExampleSet3Phase ;
+                      :hasFirstPart :ExampleSet3VariantT_TT ;
+                      :hasLastPart :ExampleSet3VariantT_TT .
+
+# As above: variant ordering to phase the genotype.
+:ExampleSet3VariantT_TT :isBefore :ExampleSet3VariantT_TT ;
+                        :isAfter :ExampleSet3VariantT_TT .
+
+# Having an instance to denote the presence of phase information
+# might appear redundant across data sets. On the other hand, it
+# permits data providers to enrich their own or other providers'
+# data set with additional information (annotations) about used
+# protocols/equipment/tools.
+:ExampleSet3Phase a :GameticPhase .
+
+# For VCF data, the type can also be &quot;ReferenceSequence&quot;, which
+# denotes that the sequence is located on a reference genome. This
+# would be indicated -- in a VCF file -- by a &quot;0&quot; in the GT field
+# (e.g., &quot;0|1&quot; (phased) or &quot;0/1&quot; (unphased) to indicate a genotype
+# whose first allele is on the reference genome and the second allele
+# is an alternative allele).
+:ExampleSet3ReferenceA_AT a :ReferenceSequence ;
+                          :hasValue &quot;A&quot; .
+
+:ExampleSet3VariantT_AT a :SequenceVariant ;
+                        :hasValue &quot;T&quot; .
+
+:ExampleSet3VariantT_TT a :SequenceVariant ;
+                        :hasValue &quot;T&quot; .
+</pre>
+          <h4 id="example4">Example 4: Encoding of a Phred Score</h4>
+          <p>Encoding of a Phred score, which is part of the GVF specification, but more widely utilized in the VCF specification.</p>
+<pre style="font-size: 10px; line-height: 13px;">
+@prefix : &lt;http://www.biointerchange.org/gfvo#&gt; .
+@prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
+
+#################################################################
+#                                                                
+#    Example 4                                                   
+#                                                                
+#    Encoding of a Phred score. GVF leaves it open how the       
+#    &quot;score&quot; (column 6) should be interpreted, but recommends    
+#    the use of Phred scores. If a data provider knows that      
+#    a Phred score was utilized, then this can be represented    
+#    via GFVO.                                                   
+#    (See &quot;Column Descriptions&quot; in the GVF specification at      
+#     http://www.sequenceontology.org/resources/gvf.html)        
+#                                                                
+#################################################################
+                                                                 
+:ExampleSet4 a :Collection ;                                     
+             :hasMember :ExampleSet4Feature1 ;                   
+             rdfs:comment &quot;Encoding of a Phred score. This example is motivated by the GVF specification, which encourages -- but does not enforce -- the use of Phred scores (http://www.sequenceontology.org/resources/gvf.html).&quot;@en .
+                                                                 
+# Interpreting &quot;score&quot; (column 6) of a GVF file as Phred score.  
+:ExampleSet4Feature1 a :Feature ;                                
+                     :hasAttribute :ExampleSet4Feature1Score .   
+                                                                 
+# Use of &quot;PhredScore&quot; instead of &quot;Score&quot; to denote the specific  
+# type of score being used.
+:ExampleSet4Feature1Score a :PhredScore ;                        
+                          :hasValue 38 .
 </pre>
 
 <h3 id="ontologyReference">Ontology Reference</h3>
 <!-- Imported via :r!~/src/Ontologies/scripts/xml2htmldocs.rb < ~/src/Ontologies/gfvo.xml -->
-
+<!-- lines 1227 -->
 <p>
   Ontology namespace "gfvo": http://www.biointerchange.org/gfvo#
 </p>
 <h4>Classes</h4>
 <p>
-  <h5 id="classAlignmentOperation">Class gfvo:AlignmentOperation</h5>
+  <h5 id="classAlias">Class "Alias"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
-  <div><i>Label:</i> Alignment Operation</div>
-  <div><i>Comment:</i> An alignment operation captures the type of alignment (see &quot;Alignment&quot; enumeration class) and alignment length between a reference sequence and target sequence. This relationship is typically expressed between a <a href="#classFeature">Feature</a> class instance and a <a href="#classTarget">Target</a> class instance. Note that an <a href="#classAlignmentOperation">Alignment Operation</a> is a list, where the order of the alignment operations is of significance.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#className">Name</a></div>
+  <div><i>Label:</i> Alias</div>
+  <div><i>Comment:</i> An alias is an alternative name whose use is mostly non-primary.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Pseudonym">http://en.wikipedia.org/wiki/Pseudonym</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classArrayComparativeGenomicHybridization">Class gfvo:ArrayComparativeGenomicHybridization</h5>
+  <h5 id="classAlleleFrequency">Class "AlleleFrequency"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
-  <div><i>Label:</i> Array Comparative Genomic Hybridization</div>
-  <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on array-comparative genomic hybridization.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuantity">Quantity</a></div>
+  <div><i>Label:</i> Allele Frequency</div>
+  <div><i>Comment:</i> Proportion of a particular gene allele in a gene pool.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Allele_frequency">http://en.wikipedia.org/wiki/Allele_frequency</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classAttribute">Class gfvo:Attribute</h5>
+  <h5 id="classAminoAcid">Class "AminoAcid"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classCustomAnnotation">CustomAnnotation</a></div>
-  <div><i>Label:</i> Attribute</div>
-  <div><i>Comment:</i> An attribute represents a tag/value pair that is not covered by either GFF3, GTF, GVF or VCF specification. For example, lowercase tags in GFF3 are permitted to allow data providers to provide additional information about a genomic feature, variant, or its meta-data. Tag/value pair attributes that are within the aforementioned specifications are expressed using classes such as <a href="#classVariant">Variant</a>, <a href="#classBreakpoint">Breakpoint</a> or <a href="#classTechnologyPlatform">Technology Platform</a>.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classChemicalEntity">ChemicalEntity</a></div>
+  <div><i>Label:</i> Amino Acid</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Amino_acid">http://en.wikipedia.org/wiki/Amino_acid</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001224">SIO_001224</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classBreakpoint">Class gfvo:Breakpoint</h5>
+  <h5 id="classAncestralSequence">Class "AncestralSequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
-  <div><i>Label:</i> Breakpoint</div>
-  <div><i>Comment:</i> A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see &quot;Breakpoint_detail&quot; in http://sequenceontology.org/resources/gvf.html).</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classReferenceSequence">ReferenceSequence</a></div>
+  <div><i>Label:</i> Ancestral Sequence</div>
+  <div><i>Comment:</i> Denotes an ancestral allele of a feature. May be used to denote the &apos;ancestral allele&apos; of VCF formatted files.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Ancestral_reconstruction">http://en.wikipedia.org/wiki/Ancestral_reconstruction</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classChromosome">Class gfvo:Chromosome</h5>
+  <h5 id="classArrayComparativeGenomicHybridization">Class "ArrayComparativeGenomicHybridization"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
-  <div><i>Label:</i> Chromosome</div>
-  <div><i>Comment:</i> A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A <a href="#classChromosome">Chromosome</a> is typically used in conjunction with <a href="#classSequencedIndividual">Sequenced Individual</a> instances. For placing genomic features (<a href="#classFeature">Feature</a> class instances) on a chromosome, contig, scaffold, etc., please see the <a href="#classLandmark">Landmark</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classGenomicAscertainingMethod">GenomicAscertainingMethod</a></div>
+  <div><i>Label:</i> Array Comparative Genomic Hybridization</div>
+  <div><i>Comment:</i> Feature provenance is based on array-comparative genomic hybridization.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classCustomAnnotation">Class gfvo:CustomAnnotation</h5>
+  <h5 id="classAttribute">Class "Attribute"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Custom Annotation</div>
-  <div><i>Comment:</i> A custom annotation is any additionally provided genomic annotation that is not covered by the GFF3, GTF, GVF or VCF specifications, and hence, not represented by any other class in the ontology. For example, in GFF3, this would typically cover the attributes with lowercase tags of column 9, which are permitted by the standard as user defined annotations.</div>
+  <div><i>Label:</i> Attribute</div>
+  <div><i>Comment:</i> An attribute denotes characteristics of an entity. At this stage, <a href="#classQuality">Quality</a> is the only direct subclass of <a href="#classAttribute">Attribute</a>, whose subclasses denote qualitative properties such as sex (<a href="#classFemale">Female</a>, <a href="#classMale">Male</a>, &quot;Mermaphrodite&quot;), zygosity (<a href="#classHemizygous">Hemizygous</a>, <a href="#classHeterozygous">Heterozygous</a>, <a href="#classHomozygous">Homozygous</a>), etc.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000614">SIO_000614</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classDNAMicroarray">Class gfvo:DNAMicroarray</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
-  <div><i>Label:</i> DNA Microarray</div>
-  <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on DNA microarray probes.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="classDNASequence">Class gfvo:DNASequence</h5>
+  <h5 id="classAverageCoverage">Class "AverageCoverage"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
-  <div><i>Label:</i> DNA Sequence</div>
-  <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on DNA sequences.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classCoverage">Coverage</a></div>
+  <div><i>Label:</i> Average Coverage</div>
+  <div><i>Comment:</i> Average coverage depth for a genomic locus (a region or single base pair), i.e. the average number of reads representing a given nucleotide in the reconstructed sequence.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage">http://en.wikipedia.org/wiki/Shotgun_sequencing#Coverage</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classDataSource">Class gfvo:DataSource</h5>
+  <h5 id="classBiologicalEntity">Class "BiologicalEntity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
-  <div><i>Label:</i> Data Source</div>
-  <div><i>Comment:</i> Provides information about the source of the data. For example, it can link out to actual sequences associated with <a href="#classFeature">Feature</a> individuals in a <a href="#classSet">Set</a>.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classMaterialEntity">MaterialEntity</a></div>
+  <div><i>Label:</i> Biological Entity</div>
+  <div><i>Comment:</i> A biological entity an entity that contains genomic material or utilizes genomic material during its existance. Genomic material itself is represented as sub-classes of Chemical Entity.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010046">SIO_010046</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classEffect">Class gfvo:Effect</h5>
+  <h5 id="classBiopolymerSequencing">Class "BiopolymerSequencing"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classVariationAnnotation">VariationAnnotation</a></div>
-  <div><i>Label:</i> Effect</div>
-  <div><i>Comment:</i> Describing the effect of a feature variant.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classGenomicAscertainingMethod">GenomicAscertainingMethod</a></div>
+  <div><i>Label:</i> Biopolymer Sequencing</div>
+  <div><i>Comment:</i> Information about features and variants is based on biopolymer sequencing.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Sequencing">http://en.wikipedia.org/wiki/Sequencing</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classFeature">Class gfvo:Feature</h5>
+  <h5 id="classBreakpoint">Class "Breakpoint"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
-  <div><i>Label:</i> Feature</div>
-  <div><i>Comment:</i> The feature class captures information about genomic sequence features. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles. A feature class instance is a composite of further information that is encoded using <a href="#classAttribute">Attribute</a>, <a href="#classReference">Reference</a>, &quot;Variation&quot; and other sub-classes of <a href="#classFeatureAnnotation">Feature Annotation</a>.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classLocus">Locus</a></div>
+  <div><i>Label:</i> Breakpoint</div>
+  <div><i>Comment:</i> A breakpoint describes the source or destination of a zero-length sequence alteration. These alterations are typically insertions, deletions or translocations according to the GVF specification (see &quot;Breakpoint_detail&quot; in http://sequenceontology.org/resources/gvf.html).</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classFeatureAnnotation">Class gfvo:FeatureAnnotation</h5>
+  <h5 id="classCatalog">Class "Catalog"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
-  <div><i>Label:</i> Feature Annotation</div>
-  <div><i>Comment:</i> A feature annotation is a class whose instances are used as composites in conjunction with <a href="#classFeature">Feature</a> class instances. The <a href="#classFeatureAnnotation">Feature Annotation</a> class is typically not used as type annotation. It rather denotes that its subclasses are to be used for extending genomic features with additional information.</div>
+  <div><i>Subclass of:</i> <a href="#classCollection">Collection</a></div>
+  <div><i>Label:</i> Catalog</div>
+  <div><i>Comment:</i> A catalog is a specialization of a <a href="#classCollection">Collection</a>, where all its contents are of the same type.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001241">SIO_001241</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classFile">Class gfvo:File</h5>
+  <h5 id="classCell">Class "Cell"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classSet">Set</a></div>
-  <div><i>Label:</i> File</div>
-  <div><i>Comment:</i> A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between <a href="#classFile">File</a> class instances should be capture with the generic <a href="#classSet">Set</a> class, which is format independent.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classBiologicalEntity">BiologicalEntity</a></div>
+  <div><i>Label:</i> Cell</div>
+  <div><i>Comment:</i> A cell is a biological unit that in itself forms a living organism or is part of a larger organism that is composed of many other cells.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Cell_(biology)">http://en.wikipedia.org/wiki/Cell_(biology)</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010001">SIO_010001</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classForwardReferenceSequenceFrameshift">Class gfvo:ForwardReferenceSequenceFrameshift</h5>
+  <h5 id="classChemicalEntity">Class "ChemicalEntity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> Forward Reference Sequence Frameshift</div>
-  <div><i>Comment:</i> Denotes a frameshift forward in the reference sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classMaterialEntity">MaterialEntity</a></div>
+  <div><i>Label:</i> Chemical Entity</div>
+  <div><i>Comment:</i> A chemical entity is an entity related to chemistry. This class is typically not instantiated, but instead, its subclasses <a href="#classAminoAcid">Amino Acid</a>, <a href="#classChromosome">Chromosome</a>, <a href="#classPeptideSequence">Peptide Sequence</a>, etc., are used to represent specific chemical entities.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010004">SIO_010004</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classFragmentReadPlatform">Class gfvo:FragmentReadPlatform</h5>
+  <h5 id="classChromosome">Class "Chromosome"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Label:</i> Fragment Read Platform</div>
-  <div><i>Comment:</i> Details about the fragment-read sequencing technology used to gather the data in a set.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classChemicalEntity">ChemicalEntity</a></div>
+  <div><i>Label:</i> Chromosome</div>
+  <div><i>Comment:</i> A chromosome is an abstract representation of an unnamed chromosome to represent ploidy within a data set. A <a href="#classChromosome">Chromosome</a> instance is used for for denoting the locus of phased genotypes. For placing genomic features (<a href="#classFeature">Feature</a> class instances) on a chromosome, contig, scaffold, etc., please see the <a href="#classLandmark">Landmark</a> class.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Chromosome">http://en.wikipedia.org/wiki/Chromosome</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000899">SIO_000899</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classGermlineFeature">Class gfvo:GermlineFeature</h5>
+  <h5 id="classCircularHelix">Class "CircularHelix"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Label:</i> Germline Feature</div>
-  <div><i>Comment:</i> The germline feature class captures information about genomic sequence features arising from germline cells.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classHelixStructure">HelixStructure</a></div>
+  <div><i>Label:</i> Circular Helix</div>
+  <div><i>Comment:</i> A circular helix structure.</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classHemizygousVariant">Class gfvo:HemizygousVariant</h5>
+  <h5 id="classCodingFrameOffset">Class "CodingFrameOffset"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Label:</i> Hemizygous Variant</div>
-  <div><i>Comment:</i> A sequence alteration with hemizygous alleles.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Coding Frame Offset</div>
+  <div><i>Comment:</i> Coding frame offset of the feature, if it is a coding sequence or feature that contributes to transcription and translation. It is referred to as &quot;frame&quot; in GTF, but called &quot;phase&quot; in GFF3 and GVF. A feature&apos;s coding frame offset can be either 0, 1, or 2.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Reading_frame">http://en.wikipedia.org/wiki/Reading_frame</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classHeterozygousVariant">Class gfvo:HeterozygousVariant</h5>
+  <h5 id="classCodonSequence">Class "CodonSequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Label:</i> Heterozygous Variant</div>
-  <div><i>Comment:</i> A sequence alteration with heterozygous alleles.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classDNASequence">DNASequence</a></div>
+  <div><i>Label:</i> Codon Sequence</div>
+  <div><i>Comment:</i> A codon sequence is a nucleotide sequence underlying a potential amino acid sequence. Codon sequences are three bases of length or multiples thereof.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Codon">http://en.wikipedia.org/wiki/Codon</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classHomozygousVariant">Class gfvo:HomozygousVariant</h5>
+  <h5 id="classCollection">Class "Collection"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Label:</i> Homozygous Variant</div>
-  <div><i>Comment:</i> A sequence alteration with homozygous alleles.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Collection</div>
+  <div><i>Comment:</i> A collection is a container for genomic data. A collection may contain information about genomic data including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by <a href="#classFile">File</a> class instances, whereas the result of unions or intersections between different <a href="#classFile">File</a> class instances should be captured within this format-independent <a href="#classCollection">Collection</a> class. When importing data whose provenance is not a GFF3, GTF, GVF or VCF file, instances of <a href="#classCollection">Collection</a> should be utilized too, or the more restrictive <a href="#classCatalog">Catalog</a> class should be used.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000616">SIO_000616</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classLandmark">Class gfvo:Landmark</h5>
+  <h5 id="classComment">Class "Comment"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
-  <div><i>Label:</i> Landmark</div>
-  <div><i>Comment:</i> A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor <a href="#classFeature">Feature</a> class instances. For expressing ploidy within a data set, please refer to the <a href="#classChromosome">Chromosome</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Comment</div>
+  <div><i>Comment:</i> A comment is a remark about a piece of information, an observation or statement. In the context of GFF3, GVF, etc., genomic feature and variation descriptions, &quot;isAfter&quot; and &quot;isBefore&quot; relationships should be used to indicate where a comment is situated between pragma or feature statements of GFF3, GTF, GVF or VCF files.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001167">SIO_001167</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classLocusAnnotation">Class gfvo:LocusAnnotation</h5>
+  <h5 id="classContig">Class "Contig"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Locus Annotation</div>
-  <div><i>Comment:</i> A locus annotation puts a genomic feature or variation in context or provides additional information about particular location related aspects that fall within a feature&apos;s range (expressed by the <a href="#objectPropertylocus">locus</a> object property of the <a href="#classFeature">Feature</a> class). The <a href="#classLocusAnnotation">Locus Annotation</a> class is not instantiated itself, but rather one of its subclasses. For example, <a href="#classLandmark">Landmark</a> is used to place a <a href="#classFeature">Feature</a> on a chromosome, scaffold, contig, or other genomic entity.</div>
+  <div><i>Subclass of:</i> <a href="#classCatalog">Catalog</a></div>
+  <div><i>Label:</i> Contig</div>
+  <div><i>Comment:</i> A contig is a contiguous DNA sequence that has been assembled from shorter overlapping DNA segments.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Contig">http://en.wikipedia.org/wiki/Contig</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classMatch">Class gfvo:Match</h5>
+  <h5 id="classCoverage">Class "Coverage"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> Match</div>
-  <div><i>Comment:</i> Denotes a match between the reference sequence and target sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuantity">Quantity</a></div>
+  <div><i>Label:</i> Coverage</div>
+  <div><i>Comment:</i> Number of nucleic acid sequence reads for a particular genomic locus (a region or single base pair).</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classMethod">Class gfvo:Method</h5>
+  <h5 id="classDNAMicroarray">Class "DNAMicroarray"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
-  <div><i>Label:</i> Method</div>
-  <div><i>Comment:</i> Information about the used scoring algorithm or method.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classGenomicAscertainingMethod">GenomicAscertainingMethod</a></div>
+  <div><i>Label:</i> DNA Microarray</div>
+  <div><i>Comment:</i> Feature information is based on DNA microarray probes.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/DNA_microarray_experiment">http://en.wikipedia.org/wiki/DNA_microarray_experiment</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001076">SIO_001076</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classPairedReadPlatform">Class gfvo:PairedReadPlatform</h5>
+  <h5 id="classDNASequence">Class "DNASequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Label:</i> Paired Read Platform</div>
-  <div><i>Comment:</i> Details about the paired-read sequencing technology used to gather the data in a set.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequence">Sequence</a></div>
+  <div><i>Label:</i> DNA Sequence</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Dna_sequence">http://en.wikipedia.org/wiki/Dna_sequence</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010016">SIO_010016</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classPhenotypeDescription">Class gfvo:PhenotypeDescription</h5>
+  <h5 id="classDNASequencing">Class "DNASequencing"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classSetAnnotation">SetAnnotation</a></div>
-  <div><i>Label:</i> Phenotype Description</div>
-  <div><i>Comment:</i> A phenotype description represents additional information about a sequenced individual&apos;s phenotype.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classBiopolymerSequencing">BiopolymerSequencing</a></div>
+  <div><i>Label:</i> DNA Sequencing</div>
+  <div><i>Comment:</i> Information about features and variants is based on DNA sequencing.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/DNA_sequencing">http://en.wikipedia.org/wiki/DNA_sequencing</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classPrenatalFeature">Class gfvo:PrenatalFeature</h5>
+  <h5 id="classExperimentalMethod">Class "ExperimentalMethod"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Label:</i> Prenatal Feature</div>
-  <div><i>Comment:</i> A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive &quot;##genomic-source&quot;, but does not describe its semantics and the referenced Logical Observation Identifiers Names and Codes (LOINC, http://loinc.org), do not define the meaning or intended usage of the term &quot;prenatal&quot; either.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classProcess">Process</a></div>
+  <div><i>Label:</i> Experimental Method</div>
+  <div><i>Comment:</i> An experimental method is a procedure that yields an experimental outcome (result). Experimental methods can be in vivo, in vitro or in silico procedures that are well described and can be referenced.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000999">SIO_000999</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classRNASequence">Class gfvo:RNASequence</h5>
+  <h5 id="classExternalReference">Class "ExternalReference"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classDataSource">DataSource</a></div>
-  <div><i>Label:</i> RNA Sequence</div>
-  <div><i>Comment:</i> A <a href="#classDataSource">Data Source</a> based on RNA sequences.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> External Reference</div>
+  <div><i>Comment:</i> A cross-reference to associate an entity to a representation in another database.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001171">SIO_001171</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classRecord">Class gfvo:Record</h5>
+  <h5 id="classFeature">Class "Feature"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> Record</div>
-  <div><i>Comment:</i> A record is an abstract representation of a genomic feature, genomic variation, or its composite elements. A record is typically not instantiated in itself, but rather its child classes (s.a. <a href="#classFeature">Feature</a>, &quot;Variation&quot;, <a href="#classReference">Reference</a>, etc.) are types for OWL individuals.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Feature</div>
+  <div><i>Comment:</i> The feature class captures information about genomic sequence features and variations. A genomic feature can be a large object, such as a chromosome or contig, down to single base-pair reference or variant alleles.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010065">SIO_010065</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classReference">Class gfvo:Reference</h5>
+  <h5 id="classFemale">Class "Female"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Reference</div>
-  <div><i>Comment:</i> Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the <a href="#classVariant">Variant</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSex">Sex</a></div>
+  <div><i>Label:</i> Female</div>
+  <div><i>Comment:</i> Denoting sex of a female individual. A female is defined as an individual producing ova.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Female">http://en.wikipedia.org/wiki/Female</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010052">SIO_010052</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classReferenceSequenceGap">Class gfvo:ReferenceSequenceGap</h5>
+  <h5 id="classFile">Class "File"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> Reference Sequence Gap</div>
-  <div><i>Comment:</i> Denotes a gap in the reference sequence for an alignment. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classCollection">Collection</a></div>
+  <div><i>Label:</i> File</div>
+  <div><i>Comment:</i> A file represents the contents of a GFF3, GTF, GVF or VCF file. It can capture genomic meta-data that is specific to any of these file formats. The result of unions, intersections or other operations between <a href="#classFile">File</a> class instances should be capture with the generic <a href="#classCollection">Collection</a> class, which is format independent, or the more restrictive <a href="#classCatalog">Catalog</a> class should be used.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000396">SIO_000396</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classReverseReferenceSequenceFrameshift">Class gfvo:ReverseReferenceSequenceFrameshift</h5>
+  <h5 id="classForwardReferenceSequenceFrameshift">Class "ForwardReferenceSequenceFrameshift"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> Reverse Reference Sequence Frameshift</div>
-  <div><i>Comment:</i> Denotes a frameshift backwards (reverse) in the reference sequence. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceAlignmentOperation">SequenceAlignmentOperation</a></div>
+  <div><i>Label:</i> Forward Reference Sequence Frameshift</div>
+  <div><i>Comment:</i> Denotes a frameshift forward in the reference sequence.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classSequencedFemale">Class gfvo:SequencedFemale</h5>
+  <h5 id="classFragmentReadPlatform">Class "FragmentReadPlatform"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Label:</i> Sequenced Female</div>
-  <div><i>Comment:</i> Aggregated sequencing information for a particular female individual. A female is defined as an individual producing ova.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequencingTechnologyPlatform">SequencingTechnologyPlatform</a></div>
+  <div><i>Label:</i> Fragment Read Platform</div>
+  <div><i>Comment:</i> Details about the fragment-read (single-end read) sequencing technology used to gather the data in a set.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classSequencedHermaphrodite">Class gfvo:SequencedHermaphrodite</h5>
+  <h5 id="classFunctionalSpecification">Class "FunctionalSpecification"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Label:</i> Sequenced Hermaphrodite</div>
-  <div><i>Comment:</i> Aggregated sequencing information for a particular individual that contains both male and female gemetes.</div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Functional Specification</div>
+  <div><i>Comment:</i> A functional specification of bioinformatics data, i.e. the specification of genomic material that potentially has biological function.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000315">SIO_000315</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classSequencedIndividual">Class gfvo:SequencedIndividual</h5>
+  <h5 id="classGameticPhase">Class "GameticPhase"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Sequenced Individual</div>
-  <div><i>Comment:</i> Aggregated sequencing information for a particular individual. Unless a sub-type of this class is used as instance type, s.a. <a href="#classSequencedFemale">Sequenced Female</a>, the sex of the individual is considered to be undetermined.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Gametic Phase</div>
+  <div><i>Comment:</i> Denotes the presence of information that required capturing the gametic phase. For diploid organisms, that means that information is available about which chromosome of a chromosome pair contributed data.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Gametic_phase">http://en.wikipedia.org/wiki/Gametic_phase</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classSequencedMale">Class gfvo:SequencedMale</h5>
+  <h5 id="classGenome">Class "Genome"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Label:</i> Sequenced Male</div>
-  <div><i>Comment:</i> Aggregated sequencing information for a particular male individual. A male is defined as an individual producing spermatozoa.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classMaterialEntity">MaterialEntity</a></div>
+  <div><i>Label:</i> Genome</div>
+  <div><i>Comment:</i> Representation of a genome. Genomic features that constitute the genome may be linked via one or more <a href="#classCollection">Collection</a>, <a href="#classCatalog">Catalog</a>, <a href="#classContig">Contig</a>, <a href="#classScaffold">Scaffold</a> or <a href="#classFile">File</a> instances.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Genome">http://en.wikipedia.org/wiki/Genome</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000984">SIO_000984</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classSet">Class gfvo:Set</h5>
+  <h5 id="classGenomeAnalysis">Class "GenomeAnalysis"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> Set</div>
-  <div><i>Comment:</i> A set is a container for genomic sequence features and related information that is independent of data provenance. A set may contain information about any genomic features including -- but not limited to -- contents of GFF3, GTF, GVF and VCF files. The latter are better represented by <a href="#classFile">File</a> class instances, whereas the result of unions or intersections between different <a href="#classFile">File</a> class instances should be captured within this format-independent <a href="#classSet">Set</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="classSetAnnotation">Class gfvo:SetAnnotation</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classRecord">Record</a></div>
-  <div><i>Label:</i> Set Annotation</div>
-  <div><i>Comment:</i> A set annotation denotes that its subclasses can be used to extend a <a href="#classSet">Set</a> with additional information, s.a. a <a href="#classPhenotypeDescription">Phenotype Description</a>. Set annotations are file format independent and can be preserved when carrying out operations between <a href="#classFile">File</a>/<a href="#classSet">Set</a> instances. Depending on the annotation, it may or may not be able to carry it over in operations such as taking the union of two or more sets, since the scope of a <a href="#classSetAnnotation">Set Annotation</a> applies to all <a href="#classFeature">Feature</a> instances within the resulting <a href="#classSet">Set</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classExperimentalMethod">ExperimentalMethod</a></div>
+  <div><i>Label:</i> Genome Analysis</div>
+  <div><i>Comment:</i> A genome analysis denotes the type of procedure that was carried out to derive information from a genome assembly.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Genomics#Genome_analysis">http://en.wikipedia.org/wiki/Genomics#Genome_analysis</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classSomaticFeature">Class gfvo:SomaticFeature</h5>
+  <h5 id="classGenomicAscertainingMethod">Class "GenomicAscertainingMethod"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Label:</i> Somatic Feature</div>
-  <div><i>Comment:</i> The somatic feature class captures information about genomic sequence features arising from somatic cells.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classExperimentalMethod">ExperimentalMethod</a></div>
+  <div><i>Label:</i> Genomic Ascertaining Method</div>
+  <div><i>Comment:</i> Provides information about the source of the data.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classStructuredAttribute">Class gfvo:StructuredAttribute</h5>
+  <h5 id="classGenotype">Class "Genotype"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classCustomAnnotation">CustomAnnotation</a></div>
-  <div><i>Label:</i> Structured Attribute</div>
-  <div><i>Comment:</i> A structured attribute denotes a tag/value pair where the value is a composite, but which is not defined in the GVF specification. The GVF specification does not explicitly permit user-defined structured attributes (see &quot;Structured Pragmas&quot; in http://sequenceontology.org/resources/gvf.html), but it is conceivable that an RDFization tool might support this use case. For some loosly defined structured data in GVF, the <a href="#classStructuredAttribute">Structured Attribute</a> class is used as well to capture the non-exhaustive list of possible data assignments of the GVF specification.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classFunctionalSpecification">FunctionalSpecification</a></div>
+  <div><i>Label:</i> Genotype</div>
+  <div><i>Comment:</i> The genotype is the genetic information captured in a particular genome. It can also refer to one or more populations, if statistical distributions are provided that assign genetic codes to groups of individuals.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001079">SIO_001079</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classTarget">Class gfvo:Target</h5>
+  <h5 id="classGenotyping">Class "Genotyping"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classLocusAnnotation">LocusAnnotation</a></div>
-  <div><i>Label:</i> Target</div>
-  <div><i>Comment:</i> A target expresses the relationship between a <a href="#classFeature">Feature</a> instance and an alignment. In GFF3, the alignment can be a nucleotide-to-nucleotide or protein-to-nucleotide (see &quot;The Gap Attribute&quot;, http://sequenceontology.org/resources/gff3.html), but this restriction is not enforced here. Note that the object property <a href="#objectPropertyalignment">alignment</a> links out to a list of <a href="#classAlignmentOperation">Alignment Operation</a> class instances, where only the first operation in that list is referenced via the <a href="#objectPropertyalignment">alignment</a> property. The remainder of operations can be accessed by stepping through the list.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classGenomeAnalysis">GenomeAnalysis</a></div>
+  <div><i>Label:</i> Genotyping</div>
+  <div><i>Comment:</i> Genotyping is the process of determining the genetics of an individual or sample. The genotype itself is expressed as the difference of genetic mark-up compared to a reference genome.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Genotyping">http://en.wikipedia.org/wiki/Genotyping</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classTargetSequenceGap">Class gfvo:TargetSequenceGap</h5>
+  <h5 id="classGermlineCell">Class "GermlineCell"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> Target Sequence Gap</div>
-  <div><i>Comment:</i> Denotes a gap in the target sequence for an alignment. The reference sequence is denoted by a <a href="#classLandmark">Landmark</a> whilst the aligned target sequence is an instance of the <a href="#classTarget">Target</a> class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classCell">Cell</a></div>
+  <div><i>Label:</i> Germline Cell</div>
+  <div><i>Comment:</i> The germline feature class captures information about genomic sequence features arising from germline cells.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Germline">http://en.wikipedia.org/wiki/Germline</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classTechnologicalAnnotation">Class gfvo:TechnologicalAnnotation</h5>
+  <h5 id="classHelixStructure">Class "HelixStructure"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Technological Annotation</div>
-  <div><i>Comment:</i> A technological annotation provides meta-data about the means that led to a genomic feature or variant discovery. This can be a provenance annotation, such as <a href="#classDataSource">Data Source</a>, it can be describing a <a href="#classMethod">Method</a>, or it can be information about the <a href="#classTechnologyPlatform">Technology Platform</a> used.</div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Helix Structure</div>
+  <div><i>Comment:</i> Helix structure denotes the physical shape of biopolymers.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/DNA_helix">http://en.wikipedia.org/wiki/DNA_helix</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="classTechnologyPlatform">Class gfvo:TechnologyPlatform</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classTechnologicalAnnotation">TechnologicalAnnotation</a></div>
-  <div><i>Label:</i> Technology Platform</div>
-  <div><i>Comment:</i> Details about the sequencing/microarray technology used to gather the data in a set.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="classVariant">Class gfvo:Variant</h5>
+  <h5 id="classHemizygous">Class "Hemizygous"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classVariationAnnotation">VariationAnnotation</a></div>
-  <div><i>Label:</i> Variant</div>
-  <div><i>Comment:</i> Describing specific sequence alterations of a genomic feature. A variant is related to <a href="#classReference">Reference</a> class instances, which denote the sequence that serves as a basis for sequence alteration comparisons.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classZygosity">Zygosity</a></div>
+  <div><i>Label:</i> Hemizygous</div>
+  <div><i>Comment:</i> A sequence alteration with hemizygous alleles.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Zygosity#Hemizygous">http://en.wikipedia.org/wiki/Zygosity#Hemizygous</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="classVariationAnnotation">Class gfvo:VariationAnnotation</h5>
+  <h5 id="classHeritage">Class "Heritage"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Subclass of:</i> <a href="#classFeatureAnnotation">FeatureAnnotation</a></div>
-  <div><i>Label:</i> Variation Annotation</div>
-  <div><i>Comment:</i> A variant annotation captures information about a genomic <a href="#classVariant">Variant</a>. A possible effect of a variant is encoded using <a href="#classEffect">Effect</a> class instances.</div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Heritage</div>
+  <div><i>Comment:</i> Heritage denotes the passing of traits from parents or ancestors. Passed traits may not be visible as a phenotype, but instead, might only manifest as genetic inheritance.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Heredity">http://en.wikipedia.org/wiki/Heredity</a></div>
   <div></div>
   </div>
 </p>
-<h4>Object Properties (Referencing other Class Instances)</h4>
 <p>
-  <h5 id="objectPropertyalignment">Object Property gfvo:alignment</h5>
+  <h5 id="classHermaphrodite">Class "Hermaphrodite"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTarget">Target</a></div>
-  <div><i>Range:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Label:</i> alignment</div>
-  <div><i>Comment:</i> An alignment is a sequence alignment between a <a href="#classFeature">Feature</a> class instance and a <a href="#classTarget">Target</a> class instance. The alignment is a list of one or more <a href="#classAlignmentOperation">Alignment Operation</a> instances that capture alignment matches, gaps and frameshifts (see &quot;The Gap Attribute&quot;, http://sequenceontology.org/resources/gff3.html).</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSex">Sex</a></div>
+  <div><i>Label:</i> Hermaphrodite</div>
+  <div><i>Comment:</i> Denoting sex of an individual that contains both male and female gametes.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Hermaphrodite">http://en.wikipedia.org/wiki/Hermaphrodite</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000784">SIO_000784</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyattributeMethod">Object Property gfvo:attributeMethod</h5>
+  <h5 id="classHeterozygous">Class "Heterozygous"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classAttribute">Attribute</a>, <a href="#classBreakpoint">Breakpoint</a>, <a href="#classEffect">Effect</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="#classMethod">Method</a></div>
-  <div><i>Label:</i> attribute method</div>
-  <div><i>Comment:</i> Further information about the <a href="#classMethod">Method</a> that is related to an attribute.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classZygosity">Zygosity</a></div>
+  <div><i>Label:</i> Heterozygous</div>
+  <div><i>Comment:</i> A sequence alteration with heterozygous alleles.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Zygosity#Heterozygous">http://en.wikipedia.org/wiki/Zygosity#Heterozygous</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyattributes">Object Property gfvo:attributes</h5>
+  <h5 id="classHomozygous">Class "Homozygous"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classAttribute">Attribute</a></div>
-  <div><i>Label:</i> attributes</div>
-  <div><i>Comment:</i> Tag name/value pair attributes of a feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classZygosity">Zygosity</a></div>
+  <div><i>Label:</i> Homozygous</div>
+  <div><i>Comment:</i> A sequence alteration with homozygous alleles.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Zygosity#Homozygous">http://en.wikipedia.org/wiki/Zygosity#Homozygous</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertybreakpoint">Object Property gfvo:breakpoint</h5>
+  <h5 id="classIdentifier">Class "Identifier"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classBreakpoint">Breakpoint</a></div>
-  <div><i>Label:</i> breakpoint</div>
-  <div><i>Comment:</i> Potential source or destination of zero-length sequence alterations.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classLabel">Label</a></div>
+  <div><i>Label:</i> Identifier</div>
+  <div><i>Comment:</i> An identifier labels an entity with a single term that is interpreted as an accession. An accession labels entities that are part of a collection of similar type.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Identifier">http://en.wikipedia.org/wiki/Identifier</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000115">SIO_000115</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertybreakpointObjectProperty">Object Property gfvo:breakpointObjectProperty</h5>
+  <h5 id="classInformationContentEntity">Class "InformationContentEntity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> breakpoint object property</div>
-  <div><i>Comment:</i> A properties that is directly associated with <a href="#classBreakpoint">Breakpoint</a> class instances.</div>
+  <div><i>Subclass of:</i> <a href="#classObject">Object</a></div>
+  <div><i>Label:</i> Information Content Entity</div>
+  <div><i>Comment:</i> An information content entity requires background information or specific domain knowledge to be interpreted correctly.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000015">SIO_000015</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertychromosome">Object Property gfvo:chromosome</h5>
+  <h5 id="classInteraction">Class "Interaction"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Range:</i> <a href="#classChromosome">Chromosome</a></div>
-  <div><i>Label:</i> chromosome</div>
-  <div><i>Comment:</i> Denotes abstract chromosome representations for capturing variants that appear on the same chromosome of a polyploid organism.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classProcess">Process</a></div>
+  <div><i>Label:</i> Interaction</div>
+  <div><i>Comment:</i> Describing interaction between features, such as the effect of a feature variant on another feature.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000593">SIO_000593</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertycontains">Object Property gfvo:contains</h5>
+  <h5 id="classLabel">Class "Label"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Label:</i> contains</div>
-  <div><i>Comment:</i> Relationship that describes which features belong to a feature set.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Label</div>
+  <div><i>Comment:</i> A label is a term or short list of terms that name an entity for the purpose of lexicographically distinguishing the entity from entities of similar type.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000179">SIO_000179</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertydataSource">Object Property gfvo:dataSource</h5>
+  <h5 id="classLandmark">Class "Landmark"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classDataSource">DataSource</a></div>
-  <div><i>Label:</i> data source</div>
-  <div><i>Comment:</i> Data source origin of the feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classIdentifier">Identifier</a></div>
+  <div><i>Label:</i> Landmark</div>
+  <div><i>Comment:</i> A landmark establishes a coordinate system for features. Landmarks can be chromosomes, contigs, scaffolds or other constructs that can harbor <a href="#classFeature">Feature</a> class instances. For expressing ploidy within a data set, please refer to the <a href="#classChromosome">Chromosome</a> class.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertydbxref">Object Property gfvo:dbxref</h5>
+  <h5 id="classLikelihood">Class "Likelihood"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classDataSource">DataSource</a>, <a href="#classFeature">Feature</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">PhenotypeDescription</a>, <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> dbxref</div>
-  <div><i>Comment:</i> A database cross-reference to associate a feature or its structured pragma metadata in GVF to a representation in another database.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuantity">Quantity</a></div>
+  <div><i>Label:</i> Likelihood</div>
+  <div><i>Comment:</i> Likelihood is the hypothetical probability of the occurrence of a certain event.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001243">SIO_001243</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyeffect">Object Property gfvo:effect</h5>
+  <h5 id="classLocus">Class "Locus"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="#classEffect">Effect</a></div>
-  <div><i>Label:</i> effect</div>
-  <div><i>Comment:</i> An effect of a particular feature variant.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> Locus</div>
+  <div><i>Comment:</i> A locus refers to a position (possibly multi-dimensional) within a genome or proteome.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Locus_(genetics)">http://en.wikipedia.org/wiki/Locus_(genetics)</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000056">SIO_000056</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyeffectObjectProperty">Object Property gfvo:effectObjectProperty</h5>
+  <h5 id="classMale">Class "Male"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> effect object property</div>
-  <div><i>Comment:</i> Properties that are directly associated with <a href="#classEffect">Effect</a> class instances.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classSex">Sex</a></div>
+  <div><i>Label:</i> Male</div>
+  <div><i>Comment:</i> Denoting sex of a male individual. A male is defined as an individual producing spermatozoa.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Male">http://en.wikipedia.org/wiki/Male</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010048">SIO_010048</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyfeatureAnnotationObjectProperty">Object Property gfvo:featureAnnotationObjectProperty</h5>
+  <h5 id="classMatch">Class "Match"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> feature annotation object property</div>
-  <div><i>Comment:</i> Property of one of the genomic annotation classes, such as <a href="#classBreakpoint">Breakpoint</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>. For properties related to the core genomic data class <a href="#classFeature">Feature</a>, see <a href="#datatypePropertyfeatureDatatypeProperty">feature datatype property</a> or <a href="#objectPropertyfeatureObjectProperty">feature object property</a>.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceAlignmentOperation">SequenceAlignmentOperation</a></div>
+  <div><i>Label:</i> Match</div>
+  <div><i>Comment:</i> Denotes a match between the reference sequence and target sequence.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyfeatureObjectProperty">Object Property gfvo:featureObjectProperty</h5>
+  <h5 id="classMaterialEntity">Class "MaterialEntity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> feature object property</div>
-  <div><i>Comment:</i> Properties that are directly associated with <a href="#classFeature">Feature</a> class instances. For properties related to <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>, or other genomic annotation classes, see <a href="#datatypePropertyfeatureAnnotationDatatypeProperty">feature annotation datatype property</a> or <a href="#objectPropertyfeatureAnnotationObjectProperty">feature annotation object property</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classObject">Object</a></div>
+  <div><i>Label:</i> Material Entity</div>
+  <div><i>Comment:</i> A material entity represents a physical object. In the context of genomic features and variations, material entities are cells, organisms, sequences, chromosomes, etc.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000004">SIO_000004</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyfeatureOntology">Object Property gfvo:featureOntology</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> feature ontology</div>
-  <div><i>Comment:</i> Explicit link-out to one or more ontologies that have been used for describing features. This is a meta comment about the URIs that link out to SO/SOFA or other ontologies.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="objectPropertyfeatureType">Object Property gfvo:featureType</h5>
+  <h5 id="classMaternalHeritage">Class "MaternalHeritage"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> feature type</div>
-  <div><i>Comment:</i> A term that is describing the sequence feature that is being affected.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classHeritage">Heritage</a></div>
+  <div><i>Label:</i> Maternal Heritage</div>
+  <div><i>Comment:</i> Maternal heritage is the passing of traits from a female to her ancestors.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Maternal_effect">http://en.wikipedia.org/wiki/Maternal_effect</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertygenomicSource">Object Property gfvo:genomicSource</h5>
+  <h5 id="classMobileElementSequenceVariant">Class "MobileElementSequenceVariant"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> genomic source</div>
-  <div><i>Comment:</i> Denotes the source of genomic data (on a cell-type level). Valid object assignments are individuals of the &quot;Genomic Source&quot; enumeration class.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceVariant">SequenceVariant</a></div>
+  <div><i>Label:</i> Mobile Element Sequence Variant</div>
+  <div><i>Comment:</i> Insertion or deletion of a mobile element. The exact modification is determined by a type of the Variation Ontology.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertygenotype">Object Property gfvo:genotype</h5>
+  <h5 id="className">Class "Name"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="#classChromosome">Chromosome</a></div>
-  <div><i>Label:</i> genotype</div>
-  <div><i>Comment:</i> Determines the genotype as observed in an individual.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classLabel">Label</a></div>
+  <div><i>Label:</i> Name</div>
+  <div><i>Comment:</i> A name assigns an entity a non-formal term (or multiples thereof) that can provide information about the entities identity.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000116">SIO_000116</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyindividual">Object Property gfvo:individual</h5>
+  <h5 id="classNote">Class "Note"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Label:</i> individual</div>
-  <div><i>Comment:</i> Links to information about an individual.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classInformationContentEntity">InformationContentEntity</a></div>
+  <div><i>Label:</i> </div>
+  <div><i>Comment:</i> A note is a short textual description.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000152">SIO_000152</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertylocus">Object Property gfvo:locus</h5>
+  <h5 id="classNumberOfReads">Class "NumberOfReads"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classBreakpoint">Breakpoint</a>, <a href="#classEffect">Effect</a>, <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classTarget">Target</a></div>
-  <div><i>Range:</i> <a href="http://biohackathon.org/resource/faldo#Region">http://biohackathon.org/resource/faldo#Region</a></div>
-  <div><i>Label:</i> locus</div>
-  <div><i>Comment:</i> The locus determines the genomic position of an genomic object. The FALDO &quot;Region&quot; class can denote genomic feature&apos;s start, stop, and strand properties, it can express fuzzy genomic ranges if exact genomic coordinates are unknown. For <a href="#classLandmark">Landmark</a> class instances, the locus provides the start and end coordinates of the landmark.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuantity">Quantity</a></div>
+  <div><i>Label:</i> Number of Reads</div>
+  <div><i>Comment:</i> Number of reads supporting a particular feature or variant.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertylocusAnnotationObjectProperty">Object Property gfvo:locusAnnotationObjectProperty</h5>
+  <h5 id="classObject">Class "Object"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> locus annotation object property</div>
-  <div><i>Comment:</i> A property related to genomic coordinates. This can be a <a href="#objectPropertylocus">locus</a> description that uses FALDO to denote Regions (with exact or probabilistic/fuzzy boundaries; <a href="#classBreakpoint">Breakpoint</a> locations) or an &quot;operation&quot; of a list of <a href="#classAlignmentOperation">Alignment Operation</a> instances that encode a CIGAR line.</div>
+  <div><i>Label:</i> Object</div>
+  <div><i>Comment:</i> An object is a concrete entity that realizes a concept and encapsulates data associated with said concept. Objects are typically representing tangible entities, such as <a href="#classChromosome">Chromosome</a>, <a href="#classDNASequence">DNA Sequence</a>, but also objects such as <a href="#classIdentifier">Identifier</a>, <a href="#classAverageCoverage">Average Coverage</a> or other computational or mathematical entities.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000776">SIO_000776</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyontologyTerm">Object Property gfvo:ontologyTerm</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> ontology term</div>
-  <div><i>Comment:</i> A cross-reference to an ontology term that is associated with a feature. For instances of the <a href="#classVariant">Variant</a> class, the associated ontology term must be a Variant Ontology term (VariO; http://purl.obolibrary.org/obo/VariO_0001 or subclasses thereof).</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="objectPropertyparent">Object Property gfvo:parent</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Label:</i> parent</div>
-  <div><i>Comment:</i> Link out to a parent feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="objectPropertyphenotypeDescription">Object Property gfvo:phenotypeDescription</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="#classPhenotypeDescription">PhenotypeDescription</a></div>
-  <div><i>Label:</i> phenotype description</div>
-  <div><i>Comment:</i> Further information about an individual&apos;s phenotype. Applies only to single individual sets.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="objectPropertyphenotypeDescriptionObjectProperty">Object Property gfvo:phenotypeDescriptionObjectProperty</h5>
+  <h5 id="classPairedEndReadPlatform">Class "PairedEndReadPlatform"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> phenotype description object property</div>
-  <div><i>Comment:</i> An object property directly associated with <a href="#classPhenotypeDescription">Phenotype Description</a> class instances.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classSequencingTechnologyPlatform">SequencingTechnologyPlatform</a></div>
+  <div><i>Label:</i> Paired End Read Platform</div>
+  <div><i>Comment:</i> Details about the paired-end read sequencing technology used to gather the data in a set.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyrecordObjectProperty">Object Property gfvo:recordObjectProperty</h5>
+  <h5 id="classPaternalHeritage">Class "PaternalHeritage"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> record object property</div>
-  <div><i>Comment:</i> A record object property is directly related to describing genomic feature or variant data. Classes that make use of record object properties are <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a>, and so on. For container classes, such as <a href="#classSet">Set</a> and <a href="#classFile">File</a>, see <a href="#objectPropertysetObjectProperty">set object property</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classHeritage">Heritage</a></div>
+  <div><i>Label:</i> Paternal Heritage</div>
+  <div><i>Comment:</i> Paternal heritage is the passing of traits from a male to his ancestors.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Maternal_effect#Paternal_effect_genes">http://en.wikipedia.org/wiki/Maternal_effect#Paternal_effect_genes</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyreference">Object Property gfvo:reference</h5>
+  <h5 id="classPeptideSequence">Class "PeptideSequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classReference">Reference</a></div>
-  <div><i>Label:</i> reference</div>
-  <div><i>Comment:</i> Specific information about the reference sequence of a feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequence">Sequence</a></div>
+  <div><i>Label:</i> Peptide Sequence</div>
+  <div><i>Comment:</i> A peptide sequence is an ordered sequence of amino acid residues, but which may not necessarily be a protein sequence. For encoding sequences of proteins, the subclass <a href="#classProteinSequence">Protein Sequence</a> should be used.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Peptide_sequence">http://en.wikipedia.org/wiki/Peptide_sequence</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyscoreMethod">Object Property gfvo:scoreMethod</h5>
+  <h5 id="classPhenotype">Class "Phenotype"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classMethod">Method</a></div>
-  <div><i>Label:</i> score method</div>
-  <div><i>Comment:</i> Used scoring method, which is described in more detail by a <a href="#classMethod">Method</a> class instance.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Phenotype</div>
+  <div><i>Comment:</i> A phenotype description represents additional information about a sequenced individual&apos;s phenotype. A sequenced individual is represented by instances of the <a href="#classSequencedIndividual">Sequenced Individual</a> class.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Phenotype">http://en.wikipedia.org/wiki/Phenotype</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010056">SIO_010056</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyseqid">Object Property gfvo:seqid</h5>
+  <h5 id="classPhredScore">Class "PhredScore"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classBreakpoint">Breakpoint</a>, <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classLandmark">Landmark</a></div>
-  <div><i>Label:</i> seqid</div>
-  <div><i>Comment:</i> Establishes the landmark on which the feature or breakpoint is located. A landmark is typically a chromosome, scaffold or contig, but can be any other genomic object (DNA, RNA, protein) in principle.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classScore">Score</a></div>
+  <div><i>Label:</i> Phred Score</div>
+  <div><i>Comment:</i> The Phred score can be used to assign quality scores to base calls of DNA sequences.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Phred_score">http://en.wikipedia.org/wiki/Phred_score</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertysequenceVariant">Object Property gfvo:sequenceVariant</h5>
+  <h5 id="classPrenatalCell">Class "PrenatalCell"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2002/07/owl#Thing">http://www.w3.org/2002/07/owl#Thing</a></div>
-  <div><i>Label:</i> sequence variant</div>
-  <div><i>Comment:</i> Effect of a sequence alteration on a sequence feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classCell">Cell</a></div>
+  <div><i>Label:</i> Prenatal Cell</div>
+  <div><i>Comment:</i> A prenatal feature is purportedly associated with prenatal cells; the GVF specification declares this feature type under the prama directive &quot;##genomic-source&quot;, but does not describe its semantics and the referenced Logical Observation Identifiers Names and Codes (LOINC, http://loinc.org), do not define the meaning or intended usage of the term &quot;prenatal&quot; either.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Prenatal">http://en.wikipedia.org/wiki/Prenatal</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertysequencedIndividualObjectProperty">Object Property gfvo:sequencedIndividualObjectProperty</h5>
+  <h5 id="classProcess">Class "Process"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> sequenced individual object property</div>
-  <div><i>Comment:</i> A property that is directly associated with <a href="#classSequencedIndividual">Sequenced Individual</a> class instances.</div>
+  <div><i>Label:</i> Process</div>
+  <div><i>Comment:</i> A process denotes a temporally dependent entity. It can be thought of as a function, where input data is transformed by an algorithm to produce certain output data.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000006">SIO_000006</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertysetAnnotationObjectProperty">Object Property gfvo:setAnnotationObjectProperty</h5>
+  <h5 id="classProteinSequence">Class "ProteinSequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> set annotation object property</div>
-  <div><i>Comment:</i> A property related to the annotation of <a href="#classSet">Set</a> class instances or its sub-classes, s.a. <a href="#classPhenotypeDescription">Phenotype Description</a>.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classPeptideSequence">PeptideSequence</a></div>
+  <div><i>Label:</i> Protein Sequence</div>
+  <div><i>Comment:</i> A protein sequence is a peptide sequence which represents the primary structure of a protein.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Peptide_sequence">http://en.wikipedia.org/wiki/Peptide_sequence</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010015">SIO_010015</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertysetObjectProperty">Object Property gfvo:setObjectProperty</h5>
+  <h5 id="classQuality">Class "Quality"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> set object property</div>
-  <div><i>Comment:</i> A property that is directly associated with the <a href="#classSet">Set</a> class. Immediate sub-properties of this property are independent to specific specifications such as GFF3, GTF, GVF or VCF. Not all sub-properties can be preserved when carrying out operations between multiple <a href="#classSet">Set</a> class instances. For example, the &quot;sex&quot; property applies to single individual sets and can only be kept in a set union between multiple <a href="#classSet">Set</a> class instances if all involved instances agree on this property. For genomic feature and variant related properties, see <a href="#objectPropertyrecordObjectProperty">record object property</a> and <a href="#datatypePropertyrecordDatatypeProperty">record datatype property</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classAttribute">Attribute</a></div>
+  <div><i>Label:</i> Quality</div>
+  <div><i>Comment:</i> Quality is a specific attribute that is strongly associated with an entity, but whose values are varying and disjunct. Qualities are finite enumerations, such as sex (<a href="#classFemale">Female</a>, <a href="#classMale">Male</a>, <a href="#classHermaphrodite">Hermaphrodite</a>), heritage (&quot;Maternal&quot;, &quot;Paternal&quot;), but they also make use of the &quot;hasValue&quot; datatype property such as <a href="#classCodingFrameOffset">Coding Frame Offset</a> (either &quot;0&quot;, &quot;1&quot; or &quot;2&quot;).</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000005">SIO_000005</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertysourceMethod">Object Property gfvo:sourceMethod</h5>
+  <h5 id="classQuantity">Class "Quantity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classMethod">Method</a></div>
-  <div><i>Label:</i> source method</div>
-  <div><i>Comment:</i> Further information about the algorithm/methodologies used.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classObject">Object</a></div>
+  <div><i>Label:</i> Quantity</div>
+  <div><i>Comment:</i> A property of a phenomenon, body, or substance, where the property has a magnitude that can be expressed by means of a number and a reference. This class is typically not directly instantiated, but instead, its subclasses <a href="#classAlleleFrequency">Allele Frequency</a>, <a href="#classAverageCoverage">Average Coverage</a>, etc. are used.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000052">SIO_000052</a></div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyspecies">Object Property gfvo:species</h5>
+  <h5 id="classRNASequencing">Class "RNASequencing"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="http://purl.obolibrary.org/obo/NCBITaxon_1">http://purl.obolibrary.org/obo/NCBITaxon_1</a></div>
-  <div><i>Label:</i> species</div>
-  <div><i>Comment:</i> NCBI Taxonomy Ontology &quot;NCBITaxon_1&quot; (or sub-classes) instance that denotes the species for a feature set.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classBiopolymerSequencing">BiopolymerSequencing</a></div>
+  <div><i>Label:</i> RNA Sequencing</div>
+  <div><i>Comment:</i> Information about features and variants is based on RNA sequencing.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/RNA-Seq">http://en.wikipedia.org/wiki/RNA-Seq</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertystructuredAttributes">Object Property gfvo:structuredAttributes</h5>
+  <h5 id="classReferenceSequence">Class "ReferenceSequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classStructuredAttribute">StructuredAttribute</a></div>
-  <div><i>Label:</i> structured attributes</div>
-  <div><i>Comment:</i> Tag name/value pair attributes that are not captured by the GVF specification.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classDNASequence">DNASequence</a></div>
+  <div><i>Label:</i> Reference Sequence</div>
+  <div><i>Comment:</i> Denotes the reference sequence of a feature. The reference sequence is of importance when dealing with genomic variation data, which is expressed by the &quot;Variant&quot; class.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Reference_sequence">http://en.wikipedia.org/wiki/Reference_sequence</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertytarget">Object Property gfvo:target</h5>
+  <h5 id="classReferenceSequenceGap">Class "ReferenceSequenceGap"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classTarget">Target</a></div>
-  <div><i>Label:</i> target</div>
-  <div><i>Comment:</i> Identifies the target that the features aligns to.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceAlignmentOperation">SequenceAlignmentOperation</a></div>
+  <div><i>Label:</i> Reference Sequence Gap</div>
+  <div><i>Comment:</i> Denotes a gap in the reference sequence for an alignment.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertytargetAttributeMethod">Object Property gfvo:targetAttributeMethod</h5>
+  <h5 id="classReverseReferenceSequenceFrameshift">Class "ReverseReferenceSequenceFrameshift"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTarget">Target</a></div>
-  <div><i>Range:</i> <a href="#classMethod">Method</a></div>
-  <div><i>Label:</i> target attribute method</div>
-  <div><i>Comment:</i> Further information about the associated attribute(s).</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceAlignmentOperation">SequenceAlignmentOperation</a></div>
+  <div><i>Label:</i> Reverse Reference Sequence Frameshift</div>
+  <div><i>Comment:</i> Denotes a frameshift backwards (reverse) in the reference sequence.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertytargetProperty">Object Property gfvo:targetProperty</h5>
+  <h5 id="classSample">Class "Sample"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> target property</div>
-  <div><i>Comment:</i> A properties that is directly associated with <a href="#classTarget">Target</a> class instances.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classChemicalEntity">ChemicalEntity</a></div>
+  <div><i>Label:</i> Sample</div>
+  <div><i>Comment:</i> A sample is a limited quantity of a chemical entity of some sort, which is typically used (destructively/non-desctructively) in a scientific analysis or test.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Sample_(material)">http://en.wikipedia.org/wiki/Sample_(material)</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_001050">SIO_001050</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertytechnologicalAnnotationObjectProperty">Object Property gfvo:technologicalAnnotationObjectProperty</h5>
+  <h5 id="classScaffold">Class "Scaffold"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> technological annotation object property</div>
-  <div><i>Comment:</i> An object property associated with annotations that are related to technological aspects regarding a genomic feature or variant. For example, a property of a <a href="#classTechnologyPlatform">Technology Platform</a> or <a href="#classDataSource">Data Source</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classCatalog">Catalog</a></div>
+  <div><i>Label:</i> Scaffold</div>
+  <div><i>Comment:</i> A scaffold is the aggregation of multiple contigs to form a larger continuous sequencing region.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Contig">http://en.wikipedia.org/wiki/Contig</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertytechnologyPlatform">Object Property gfvo:technologyPlatform</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Label:</i> technology platform</div>
-  <div><i>Comment:</i> Technology platform that was used to derive the feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="objectPropertytype">Object Property gfvo:type</h5>
+  <h5 id="classScore">Class "Score"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.sequenceontology.org/miso/current_release/term/SO:0000110">http://www.sequenceontology.org/miso/current_release/term/SO:0000110</a></div>
-  <div><i>Label:</i> type</div>
-  <div><i>Comment:</i> Type of the feature, which is a child entry of sequence_feature (SO:0000110) of the full Sequence Ontology (SO).</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classObject">Object</a></div>
+  <div><i>Label:</i> Score</div>
+  <div><i>Comment:</i> A measure that permits the ranking of entities.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Score_(statistics)">http://en.wikipedia.org/wiki/Score_(statistics)</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyvariant">Object Property gfvo:variant</h5>
+  <h5 id="classSequence">Class "Sequence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Label:</i> variant</div>
-  <div><i>Comment:</i> Specific information about the variant(s) of a feature.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classChemicalEntity">ChemicalEntity</a></div>
+  <div><i>Label:</i> Sequence</div>
+  <div><i>Comment:</i> A sequence provides information about any biopolymer sequences. Specialized subclasses are provided to denote specialized instances of sequences, such as <a href="#classCodonSequence">Codon Sequence</a>, <a href="#classReferenceSequence">Reference Sequence</a>, <a href="#classProteinSequence">Protein Sequence</a>, etc.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000030">SIO_000030</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyvariantObjectProperty">Object Property gfvo:variantObjectProperty</h5>
+  <h5 id="classSequenceAlignment">Class "SequenceAlignment"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> variant object property</div>
-  <div><i>Comment:</i> Properties that are directly associated with <a href="#classVariant">Variant</a> class instances.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classObject">Object</a></div>
+  <div><i>Label:</i> Sequence Alignment</div>
+  <div><i>Comment:</i> A sequence alignment denotes the congruence of two sequences.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Sequence_alignment">http://en.wikipedia.org/wiki/Sequence_alignment</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span></div>
   </div>
 </p>
 <p>
-  <h5 id="objectPropertyvariationAnnotationObjectProperty">Object Property gfvo:variationAnnotationObjectProperty</h5>
+  <h5 id="classSequenceAlignmentOperation">Class "SequenceAlignmentOperation"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> variation annotation object property</div>
-  <div><i>Comment:</i> A variation annotation object property is describing an object property of a <a href="#classVariant">Variant</a> or <a href="#classEffect">Effect</a> class instance.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classExperimentalMethod">ExperimentalMethod</a></div>
+  <div><i>Label:</i> Sequence Alignment Operation</div>
+  <div><i>Comment:</i> A sequence alignment operation captures the type of alignment (see <a href="#classSequenceAlignment">Sequence Alignment</a>) between a reference sequence and target sequence. Note that an &quot;Alignment Operation&quot; is situated in a linked list, where the order of the alignment operations is of significance.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Sequence_alignment">http://en.wikipedia.org/wiki/Sequence_alignment</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
-<h4>Datatype Properties (Strings, Numbers, Dates, etc.)</h4>
 <p>
-  <h5 id="datatypeProperty3primeContext">Datatype Property gfvo:3primeContext</h5>
+  <h5 id="classSequenceVariant">Class "SequenceVariant"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> 3&apos; context</div>
-  <div><i>Comment:</i> Sequence context of a feature on the positive strand (forward strand) on the 3&apos; end. A valid sequence context is denoted by a string of one or more concatenated letters A, C, G, or T.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classDNASequence">DNASequence</a></div>
+  <div><i>Label:</i> Sequence Variant</div>
+  <div><i>Comment:</i> Describing specific sequence alterations of a genomic feature. A variant is related to &quot;Reference&quot; class instances, which denote the sequence that serves as a basis for sequence alteration comparisons.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Mutation">http://en.wikipedia.org/wiki/Mutation</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypeProperty5primeContext">Datatype Property gfvo:5primeContext</h5>
+  <h5 id="classSequencedIndividual">Class "SequencedIndividual"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> 5&apos; context</div>
-  <div><i>Comment:</i> Sequence context of a feature on the positive strand (forward strand) on the 5&apos; end. A valid sequence context is denoted by a string of one or more concatenated letters A, C, G, or T.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classBiologicalEntity">BiologicalEntity</a></div>
+  <div><i>Label:</i> Sequenced Individual</div>
+  <div><i>Comment:</i> Aggregated sequencing information for a particular individual.</div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010000">SIO_010000</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyalias">Datatype Property gfvo:alias</h5>
+  <h5 id="classSequencingTechnologyPlatform">Class "SequencingTechnologyPlatform"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> alias</div>
-  <div><i>Comment:</i> Secondary name of a feature besides the primary feature ID. The secondary name can be a HGVS/ISCN nomenclature name, but not a cross-reference to a database (e.g. dbSNP, OMIM). Cross-references should be made using the <a href="#objectPropertydbxref">dbxref</a> property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classGenomicAscertainingMethod">GenomicAscertainingMethod</a></div>
+  <div><i>Label:</i> Sequencing Technology Platform</div>
+  <div><i>Comment:</i> Details about the sequencing/microarray technology used to gather the data in a set.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Read_(Biology)">http://en.wikipedia.org/wiki/Read_(Biology)</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyalignmentOperationDatatypeProperty">Datatype Property gfvo:alignmentOperationDatatypeProperty</h5>
+  <h5 id="classSex">Class "Sex"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> alignment operation datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with <a href="#classAlignmentOperation">Alignment Operation</a> instances.</div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Sex</div>
+  <div><i>Comment:</i> Biological sex of an individual.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Sex">http://en.wikipedia.org/wiki/Sex</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_010029">SIO_010029</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyaminoAcid">Datatype Property gfvo:aminoAcid</h5>
+  <h5 id="classSomaticCell">Class "SomaticCell"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> amino acid</div>
-  <div><i>Comment:</i> Amino acid in the reference genome that overlaps with a variant&apos;s genome coordinates.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Subclass of:</i> <a href="#classCell">Cell</a></div>
+  <div><i>Label:</i> Somatic Cell</div>
+  <div><i>Comment:</i> The somatic feature class captures information about genomic sequence features arising from somatic cells.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Somatic">http://en.wikipedia.org/wiki/Somatic</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyaverageCoverage">Datatype Property gfvo:averageCoverage</h5>
+  <h5 id="classSpan">Class "Span"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> average coverage</div>
-  <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classQuantity">Quantity</a></div>
+  <div><i>Label:</i> Span</div>
+  <div><i>Comment:</i> A span is an attribute denoting the number of nucleotides or peptides that an entity covers. This is directly used in conjunction with <a href="#classSequenceAlignmentOperation">Sequence Alignment Operation</a> subclasses, e.g. to express the number of nucleotides a sequence alignment match ranges over.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertybuild">Datatype Property gfvo:build</h5>
+  <h5 id="classTargetSequenceGap">Class "TargetSequenceGap"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSet">Set</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> build</div>
-  <div><i>Comment:</i> Name of a genome assembly build that denotes the provenance of genomic features and variants in a <a href="#classSet">Set</a>. For example, &apos;GRCh37&apos;, &apos;NCBI 36&apos;, &apos;FlyBase r4.1&apos;, or &apos;hg19&apos;. If possible, the patch level of the assembly build should be included, such as &apos;GRCh37.p7&apos;.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classSequenceAlignmentOperation">SequenceAlignmentOperation</a></div>
+  <div><i>Label:</i> Target Sequence Gap</div>
+  <div><i>Comment:</i> Denotes a gap in the target sequence for an alignment.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertycodon">Datatype Property gfvo:codon</h5>
+  <h5 id="classTotalNumberOfReads">Class "TotalNumberOfReads"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> codon</div>
-  <div><i>Comment:</i> Describes the codon from the reference sequence whose coordinates overlap with this variant. A valid codon description is a string of three -- or multiples thereof -- concatenated letters A, C, G, or T.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Subclass of:</i> <a href="#classNumberOfReads">NumberOfReads</a></div>
+  <div><i>Label:</i> Total Number of Reads</div>
+  <div><i>Comment:</i> Total number of reads covering a feature or variant.</div>
+  <div><span style="margin-right: 4px;" class="badge alert-success">GVF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertycomment">Datatype Property gfvo:comment</h5>
+  <h5 id="classVariantCalling">Class "VariantCalling"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classDataSource">DataSource</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">PhenotypeDescription</a>, <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> comment</div>
-  <div><i>Comment:</i> Comments should be made using &quot;http://www.w3.org/2000/01/rdf-schema#comment&quot;.This datatype property only exists to redirect the focus to RDF Schema for commenting, since it might be expected that comments are modeled similar to other datatype properties involving <a href="#classDataSource">Data Source</a>, <a href="#classMethod">Method</a>, <a href="#classPhenotypeDescription">Phenotype Description</a> or <a href="#classTechnologyPlatform">Technology Platform</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classGenomeAnalysis">GenomeAnalysis</a></div>
+  <div><i>Label:</i> Variant Calling</div>
+  <div><i>Comment:</i> Denotes the technique of calling genomic feature variants in a genome assembly.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data">http://en.wikipedia.org/wiki/SNV_calling_from_NGS_data</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertycustomAnnotationDatatypeProperty">Datatype Property gfvo:customAnnotationDatatypeProperty</h5>
+  <h5 id="classVersion">Class "Version"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> custom annotation datatype property</div>
-  <div><i>Comment:</i> Datatype property of an <a href="#classAttribute">Attribute</a> or <a href="#classStructuredAttribute">Structured Attribute</a> class instance. <a href="#classAttribute">Attribute</a> and <a href="#classStructuredAttribute">Structured Attribute</a> class instances are used to capture genomic feature and variation data assignments that may appear in a GFF3, GTF, GVF or VCF file, but which are not covered by their respective specifications.</div>
-  <div></div>
+  <div><i>Subclass of:</i> <a href="#classIdentifier">Identifier</a></div>
+  <div><i>Label:</i> Version</div>
+  <div><i>Comment:</i> A version names a release of a software, dataset, or other resource. A versioned resource is not necessarily public.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Versioning">http://en.wikipedia.org/wiki/Versioning</a></div>
+  <div><i>Semanticscience Integrated Ontology class equivalence:</i> <a href="http://bioportal.bioontology.org/ontologies/SIO/?p=classes&conceptid=http%3A%2F%2Fsemanticscience.org%2Fresource%2FSIO_000653">SIO_000653</a></div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyeffectDatatypeProperty">Datatype Property gfvo:effectDatatypeProperty</h5>
+  <h5 id="classWatsonCrickHelix">Class "WatsonCrickHelix"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> effect datatype property</div>
-  <div><i>Comment:</i> A datatype property that are directly associated with <a href="#classEffect">Effect</a> class instances.</div>
+  <div><i>Subclass of:</i> <a href="#classHelixStructure">HelixStructure</a></div>
+  <div><i>Label:</i> Watson-Crick Helix</div>
+  <div><i>Comment:</i> Helical structure as first proposed by Watson and Crick.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Non-helical_models_of_DNA_structure#Proposal_of_Watson.E2.80.93Crick_helical_structure">http://en.wikipedia.org/wiki/Non-helical_models_of_DNA_structure#Proposal_of_Watson.E2.80.93Crick_helical_structure</a></div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyfeature">Datatype Property gfvo:feature</h5>
+  <h5 id="classZygosity">Class "Zygosity"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classEffect">Effect</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> feature</div>
-  <div><i>Comment:</i> Features that are affected by this sequence alteration effect. This can be an external feature identifier, such as an Ensembl gene/transcript identifier.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertyfeatureAnnotationDatatypeProperty">Datatype Property gfvo:featureAnnotationDatatypeProperty</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> feature annotation datatype property</div>
-  <div><i>Comment:</i> Property of one of the genomic annotation classes, such as <a href="#classBreakpoint">Breakpoint</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>. For properties related to the core genomic data class <a href="#classFeature">Feature</a>, see <a href="#datatypePropertyfeatureDatatypeProperty">feature datatype property</a> or <a href="#objectPropertyfeatureObjectProperty">feature object property</a>.</div>
+  <div><i>Subclass of:</i> <a href="#classQuality">Quality</a></div>
+  <div><i>Label:</i> Zygosity</div>
+  <div><i>Comment:</i> Zygosity denotes the similarities of a specific allele in the genome of an organism.</div>
+  <div><i>Wikipedia reference:</i> <a href="http://en.wikipedia.org/wiki/Zygosity">http://en.wikipedia.org/wiki/Zygosity</a></div>
   <div></div>
   </div>
 </p>
+<h4>Object Properties</h4>
 <p>
-  <h5 id="datatypePropertyfeatureDatatypeProperty">Datatype Property gfvo:featureDatatypeProperty</h5>
+  <h5 id="objectPropertydescribes">Object Property "describes"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> feature datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with a <a href="#classFeature">Feature</a> class instance. For properties related to <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a>, or other genomic annotation classes, see <a href="#datatypePropertyfeatureAnnotationDatatypeProperty">feature annotation datatype property</a> or <a href="#objectPropertyfeatureAnnotationObjectProperty">feature annotation object property</a>.</div>
+  <div><i>Label:</i> describes</div>
+  <div><i>Comment:</i> Links to an entity for which supportive information is being provided.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000563</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyfileDatatypeProperty">Datatype Property gfvo:fileDatatypeProperty</h5>
+  <h5 id="objectPropertyhasAnnotation">Object Property "hasAnnotation"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> file datatype property</div>
-  <div><i>Comment:</i> Datatype properties related to <a href="#classFile">File</a> class instances. Subclasses of this property are used for denoting data that is specific to files only and which is only preserved as a means to encode for all data items defined by the GFF3, GTF, GVF and VCF specifications. These properties cannot be carried over into the result of set operations (s.a. union) between <a href="#classFile">File</a>/<a href="#classSet">Set</a> class instances. Keeping these properties in the result set between set operations may result in wrong annotations or contradictions (e.g., mutliple assignment of different versions or dates).</div>
+  <div><i>Label:</i> has annotation</div>
+  <div><i>Comment:</i> Links to additional annotations about an entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000255</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyfileDate">Datatype Property gfvo:fileDate</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#dateTime">http://www.w3.org/2001/XMLSchema#dateTime</a></div>
-  <div><i>Label:</i> file date</div>
-  <div><i>Comment:</i> Creation date of the data file whose genomic data is captured by the associated <a href="#classFile">File</a> instance.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertyfileVersion">Datatype Property gfvo:fileVersion</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> file version</div>
-  <div><i>Comment:</i> Proprietary version of the file or its contents whose genomic data is associated with a <a href="#classFile">File</a> instance.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertyfrequency">Datatype Property gfvo:frequency</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div><i>Label:</i> frequency</div>
-  <div><i>Comment:</i> Frequency of a variant in a population. The population is determined by the <a href="#classSet">Set</a> in which the <a href="#classVariant">Variant</a> resides.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertygffVersion">Datatype Property gfvo:gffVersion</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> gff version</div>
-  <div><i>Comment:</i> Version of the GFF3 specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 3.0, but less than 4.0. For GFF2/GTF version number assignment, see the <a href="#datatypePropertygtfVersion">gtf version</a> datatype property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertygtfVersion">Datatype Property gfvo:gtfVersion</h5>
-  <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> gtf version</div>
-  <div><i>Comment:</i> Version of the GTF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 2.0, but less than 3.0. This number derives from the fact that GTF files are equivalent to GFF2 files. GTF/GFF2 files are incompatible with the GFF3 specification. For GFF3 version number assignment, see the <a href="#datatypePropertygffVersion">gff version</a> datatype property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-info">GTF</span></div>
-  </div>
-</p>
-<p>
-  <h5 id="datatypePropertygvfVersion">Datatype Property gfvo:gvfVersion</h5>
+  <h5 id="objectPropertyhasAttribute">Object Property "hasAttribute"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> gvf version</div>
-  <div><i>Comment:</i> Version of the GVF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 1.0, but less than 2.0. GVF files usually make a statement about their underlying GFF3 specification that they rely on too, which should be encoded using the <a href="#datatypePropertygffVersion">gff version</a> datatype property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has attribute</div>
+  <div><i>Comment:</i> Links out to aggregate information for an entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000008</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyid">Datatype Property gfvo:id</h5>
+  <h5 id="objectPropertyhasEvidence">Object Property "hasEvidence"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classTarget">Target</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> id</div>
-  <div><i>Comment:</i> A unique identifier for the feature within the feature set (a <a href="#classSet">Set</a>/<a href="#classFile">File</a> class instance). The unique identifier is important when dealing with GFF3, GTF, GVF or VCF files as a stand in object that makes the aggregation and separation of genomic feature and variant information possible. In RDF, the URI of subject should be used primarily, provided that its URI can be considered stable.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Label:</i> has evidence</div>
+  <div><i>Comment:</i> References an entity or resource that provides supporting/refuting evidence.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000772</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyisCircular">Datatype Property gfvo:isCircular</h5>
+  <h5 id="objectPropertyhasFirstPart">Object Property "hasFirstPart"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#boolean">http://www.w3.org/2001/XMLSchema#boolean</a></div>
-  <div><i>Label:</i> </div>
-  <div><i>Comment:</i> Truth value describing whether the feature is circular or not. This can be used to describe, for example, circular DNA as being found in bacteria or viruses. It can also be applied to mitochondrial DNA or plastid DNA, where applicable.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has first part</div>
+  <div><i>Comment:</i> Denotes the first entity of an ordered part relationship.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000971</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyisPhased">Datatype Property gfvo:isPhased</h5>
+  <h5 id="objectPropertyhasIdentifier">Object Property "hasIdentifier"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#boolean">http://www.w3.org/2001/XMLSchema#boolean</a></div>
-  <div><i>Label:</i> is phased</div>
-  <div><i>Comment:</i> Indicates whether this particular feature is phased. Used to encode &quot;##phased-genotypes&quot; statements in GFF3, but can be appropriated freely. It is also a property of GVF variants, even though the GVF specification is unclear on its exact usage details.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has identifier</div>
+  <div><i>Comment:</i> Links out to an identifier.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000671</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertylandmarkDatatypeProperty">Datatype Property gfvo:landmarkDatatypeProperty</h5>
+  <h5 id="objectPropertyhasInput">Object Property "hasInput"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> landmark datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with <a href="#classLandmark">Landmark</a> class instances.</div>
+  <div><i>Label:</i> has input</div>
+  <div><i>Comment:</i> Links out to an entity that is the input of a <a href="#classProcess">Process</a> subclass.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000230</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertylocusAnnotationDatatypeProperty">Datatype Property gfvo:locusAnnotationDatatypeProperty</h5>
+  <h5 id="objectPropertyhasLastPart">Object Property "hasLastPart"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> locus annotation datatype property</div>
-  <div><i>Comment:</i> A property related to, or associated with, genomic coordinates. This can be a genomic <a href="#datatypePropertysequence">sequence</a> description, the <a href="#datatypePropertyfrequency">frequency</a> of a <a href="#classVariant">Variant</a>, <a href="#datatypePropertyphredScore">phred score</a> of either <a href="#classVariant">Variant</a> or <a href="#classReference">Reference</a>, etc.</div>
+  <div><i>Label:</i> has last part</div>
+  <div><i>Comment:</i> Denotes the last entity of an ordered part relationship.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000972</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyname">Datatype Property gfvo:name</h5>
+  <h5 id="objectPropertyhasMember">Object Property "hasMember"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> name</div>
-  <div><i>Comment:</i> Name of a feature, which can be used for display purposes. The name is not a unique property among features in a <a href="#classSet">Set</a>.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has member</div>
+  <div><i>Comment:</i> Denotes membership for <a href="#classCollection">Collection</a>, <a href="#classCatalog">Catalog</a> and <a href="#classFile">File</a> instances.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000059</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertynote">Datatype Property gfvo:note</h5>
+  <h5 id="objectPropertyhasOrderedPart">Object Property "hasOrderedPart"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> note</div>
-  <div><i>Comment:</i> Free text notes should be made using &quot;http://www.w3.org/2000/01/rdf-schema#comment&quot;.This datatype property only exists to redirect the focus to RDF Schema for annotating features with notes, since it might be expected that a note is similarly modeled to other datatype properties of the <a href="#classFeature">Feature</a> class.</div>
+  <div><i>Label:</i> has ordered part</div>
+  <div><i>Comment:</i> Denotes a compositional relationship to other entities, where the ordering of the composition of entities carries meaning.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000974</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyphase">Datatype Property gfvo:phase</h5>
+  <h5 id="objectPropertyhasOutput">Object Property "hasOutput"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> phase</div>
-  <div><i>Comment:</i> Phase of the feature, if it is a CDS. Called &quot;frame&quot; in GTF. A feature&apos;s phase can be either 0, 1, or 2.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has output</div>
+  <div><i>Comment:</i> Links out to an entity that is the output of a <a href="#classProcess">Process</a> subclass.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000229</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyphredScore">Datatype Property gfvo:phredScore</h5>
+  <h5 id="objectPropertyhasPart">Object Property "hasPart"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#double">http://www.w3.org/2001/XMLSchema#double</a></div>
-  <div><i>Label:</i> phred score</div>
-  <div><i>Comment:</i> A phred-scaled quality score for the reference seuence; -10log_10 prob(no variant). A phred-scaled quality score for a variant sequence; -10log_10 prob(variant call is wrong). High scores indicate high confidence calls. This is a property associated with VCF data. E-values and P-values of features should be expressed using the <a href="#datatypePropertyscore">score</a> datatype property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Label:</i> has part</div>
+  <div><i>Comment:</i> Denotes a compositional relationship to other entities.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000028</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyplatformClass">Datatype Property gfvo:platformClass</h5>
+  <h5 id="objectPropertyhasParticipant">Object Property "hasParticipant"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> platform class</div>
-  <div><i>Comment:</i> Type of technology used to gather the variant data. The GVF specification&apos;s list of available classes is naturally incomplete. The range of this property is therefore unrestricted due to its open specification.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has participant</div>
+  <div><i>Comment:</i> Denotes the participation of other entities in processes.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000132</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyplatformName">Datatype Property gfvo:platformName</h5>
+  <h5 id="objectPropertyhasQuality">Object Property "hasQuality"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> platform name</div>
-  <div><i>Comment:</i> Sequencer or other machine used to collect the variant data. The GVF specification&apos;s list of available platforms is naturally incomplete. The range of this property is therefore unrestricted due to its open specification.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has quality</div>
+  <div><i>Comment:</i> Links out to an entity that provides qualitative information.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000217</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyreadIPairSpan">Datatype Property gfvo:readIPairSpan</h5>
+  <h5 id="objectPropertyhasSource">Object Property "hasSource"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> read pair span</div>
-  <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> has source</div>
+  <div><i>Comment:</i> Denotes information origin.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000253</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyreadLength">Datatype Property gfvo:readLength</h5>
+  <h5 id="objectPropertyisAbout">Object Property "isAbout"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classTechnologyPlatform">TechnologyPlatform</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> read length</div>
-  <div><i>Comment:</i> Undocumented in GVF specification. Even though the property&apos;s semantics are undocumented, it is still included in the ontology in order to reflect the data values that might be encoded in GVF files.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is about</div>
+  <div><i>Comment:</i> References an entity about which information is provided for.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000332</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyreads">Datatype Property gfvo:reads</h5>
+  <h5 id="objectPropertyisAffectedBy">Object Property "isAffectedBy"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> reads</div>
-  <div><i>Comment:</i> Number of reads that are supporting a variant. Valid values are integers greater or equal than zero.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is affected by</div>
+  <div><i>Comment:</i> Denotes that an entity is affected by another entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_001159</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyrecordDatatypeProperty">Datatype Property gfvo:recordDatatypeProperty</h5>
+  <h5 id="objectPropertyisAfter">Object Property "isAfter"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> record datatype property</div>
-  <div><i>Comment:</i> A record datatype property is directly related to describing genomic feature or variant data. Classes that make use of record datatype properties are <a href="#classFeature">Feature</a>, <a href="#classVariant">Variant</a>, and so on. For container classes, such as <a href="#classSet">Set</a> and <a href="#classFile">File</a>, see <a href="#datatypePropertysetDatatypeProperty">set datatype property</a>.</div>
+  <div><i>Label:</i> is after</div>
+  <div><i>Comment:</i> Denotes the trailing occurrence or succession of the subject in regards to the object.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000211</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyreferenceAnnotationDatatypeProperty">Datatype Property gfvo:referenceAnnotationDatatypeProperty</h5>
+  <h5 id="objectPropertyisAttributeOf">Object Property "isAttributeOf"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> reference annotation datatype property</div>
-  <div><i>Comment:</i> Property that is related to a <a href="#classReference">Reference</a> class instance. This property can also be applied to <a href="#classVariant">Variant</a> class instances, which share the same datatype description, but differ in their semantic interpretation of a genomic feature.</div>
+  <div><i>Label:</i> is attribute of</div>
+  <div><i>Comment:</i> Denotes that an entity is an attribute of the entity that this property links out to.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000011</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyscore">Datatype Property gfvo:score</h5>
+  <h5 id="objectPropertyisBefore">Object Property "isBefore"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div><i>Label:</i> score</div>
-  <div><i>Comment:</i> Score of the feature. For example, an E-value for sequence similarity features or a P-value for ab initio gene prediction features. Phred scores that are associated with reference- or variant-sequences should be encoded using the <a href="#datatypePropertyphredScore">phred score</a> datatype property.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is before</div>
+  <div><i>Comment:</i> Denotes the leading occurrence or precedence of the subject in regards to the object.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000240</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertysequence">Datatype Property gfvo:sequence</h5>
+  <h5 id="objectPropertyisCreatedBy">Object Property "isCreatedBy"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a>, <a href="#classLandmark">Landmark</a>, <a href="#classReference">Reference</a>, <a href="#classVariant">Variant</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> sequence</div>
-  <div><i>Comment:</i> All sequence variations at a locus -- including the reference sequence when appropriate (for example, when the locus is heterozygous). If the feature is on the minus strand, then the sequence is the reverse-compliment of the reference genome for these coordinates.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is created by</div>
+  <div><i>Comment:</i> Denotes the process or method that created an entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000365</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertysequencedIndividualDatatypeProperty">Datatype Property gfvo:sequencedIndividualDatatypeProperty</h5>
+  <h5 id="objectPropertyisDescribedBy">Object Property "isDescribedBy"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> sequenced individual datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with <a href="#classSequencedIndividual">Sequenced Individual</a> class instances.</div>
+  <div><i>Label:</i> is described by</div>
+  <div><i>Comment:</i> Provides a description of the subject via reference to an object that provides further information on the subject.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000557</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertysetDatatypeProperty">Datatype Property gfvo:setDatatypeProperty</h5>
+  <h5 id="objectPropertyisLocatedOn">Object Property "isLocatedOn"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> set datatype property</div>
-  <div><i>Comment:</i> A property that is directly associated with the <a href="#classSet">Set</a> class. Immediate sub-properties of this property are independent to specific specifications such as GFF3, GTF, GVF or VCF. Not all sub-properties can be preserved when carrying out operations between multiple <a href="#classSet">Set</a> class instances. For example, the <a href="#datatypePropertybuild">build</a> property can only be kept in a set union between multiple <a href="#classSet">Set</a> class instances if all involved instances agree on this property. For genomic feature and variant related properties, see <a href="#objectPropertyrecordObjectProperty">record object property</a> and <a href="#datatypePropertyrecordDatatypeProperty">record datatype property</a>.</div>
+  <div><i>Label:</i> is located on</div>
+  <div><i>Comment:</i> Denotes the location of genomic feature on a landmark.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000061</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertysource">Datatype Property gfvo:source</h5>
+  <h5 id="objectPropertyisPartOf">Object Property "isPartOf"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFeature">Feature</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> source</div>
-  <div><i>Comment:</i> A free text qualifier that describes the algorithm or operating procedure that generated this feature.  For example, the name of the software that generated this feature or a database name.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is part of</div>
+  <div><i>Comment:</i> Denotes that an entity is an intrinsic component of an encapsulating entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000068</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyspan">Datatype Property gfvo:span</h5>
+  <h5 id="objectPropertyisParticipantIn">Object Property "isParticipantIn"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classAlignmentOperation">AlignmentOperation</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> span</div>
-  <div><i>Comment:</i> A span denotes the number of continuous nucleotides or amino acids an <a href="#classAlignmentOperation">Alignment Operation</a> is annotating. A span can be of length zero or greater.</div>
+  <div><i>Label:</i> is participant in</div>
+  <div><i>Comment:</i> Denotes participation with another entity.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000062</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertytag">Datatype Property gfvo:tag</h5>
+  <h5 id="objectPropertyisRefutedBy">Object Property "isRefutedBy"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classAttribute">Attribute</a>, <a href="#classStructuredAttribute">StructuredAttribute</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#string">http://www.w3.org/2001/XMLSchema#string</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> tag</div>
-  <div><i>Comment:</i> Tag name of a feature attribute. <a href="#classAttribute">Attribute</a> and <a href="#classStructuredAttribute">Structured Attribute</a> instances are key/value(s) pairs, The key in that assignment is referred to as the <a href="#datatypePropertytag">tag</a>. Custom annotations, i.e. attributes that are not defined by the file format specifications, should use lowercase tags. Future extensions of the specifications might introduce new attributes though, which can be encoded using custom annotations by RDFization tools. The tag should therefore not be treated as strictly lowercase when dealing with custom annotations.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-important">GFF3</span><span style="margin-right: 4px;" class="badge badge-info">GTF</span><span style="margin-right: 4px;" class="badge badge-success">GVF</span><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Label:</i> is refuted by</div>
+  <div><i>Comment:</i> References an entity or resource that provides refuting evidence.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000774</div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertytargetDatatypeProperty">Datatype Property gfvo:targetDatatypeProperty</h5>
+  <h5 id="objectPropertyisSourceOf">Object Property "isSourceOf"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> target datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with <a href="#classTarget">Target</a> class instances.</div>
+  <div><i>Label:</i> is source of</div>
+  <div><i>Comment:</i> Denotes that an entity is the source of the entity that this property links out to.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000219</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertytechnologicalAnnotationDatatypeProperty">Datatype Property gfvo:technologicalAnnotationDatatypeProperty</h5>
+  <h5 id="objectPropertyisSpatiotemporallyRelatedTo">Object Property "isSpatiotemporallyRelatedTo"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> technological annotation datatype property</div>
-  <div><i>Comment:</i> A datatype property associated with annotations that are related to technological aspects regarding a genomic feature or variant. For example, a property of a <a href="#classTechnologyPlatform">Technology Platform</a> class instance.</div>
+  <div><i>Label:</i> is spatiotemporally related to</div>
+  <div><i>Comment:</i> Denotes spatio-temporal relations to other entities.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000322</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertytechnologyPlatformDatatypeProperty">Datatype Property gfvo:technologyPlatformDatatypeProperty</h5>
+  <h5 id="objectPropertyisSupportedBy">Object Property "isSupportedBy"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> technology platform datatype property</div>
-  <div><i>Comment:</i> Property that is directly associated with <a href="#classTechnologyPlatform">Technology Platform</a> class instances.</div>
+  <div><i>Label:</i> is supported by</div>
+  <div><i>Comment:</i> References an entity or resource that provides supporting evidence.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000206</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertytotalReads">Datatype Property gfvo:totalReads</h5>
+  <h5 id="objectPropertyisTemporarilyPartOf">Object Property "isTemporarilyPartOf"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classSequencedIndividual">SequencedIndividual</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#int">http://www.w3.org/2001/XMLSchema#int</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> total reads</div>
-  <div><i>Comment:</i> Total number of reads for a <a href="#classSequencedIndividual">Sequenced Individual</a>. When merging <a href="#classSet">Set</a>/<a href="#classFile">File</a> class instances, it should be noted whether the total number of reads needs to be updated based on the identity of sequenced individuals in the involved sets.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-success">GVF</span></div>
+  <div><i>Label:</i> is temporarily part of</div>
+  <div><i>Comment:</i> Denotes a temporarily constraint &quot;isPartOf&quot; relationship. The temporal restriction expresses that the relationship is not universally true.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> </div>
+  <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyvariant_datatype_property">Datatype Property gfvo:variant_datatype_property</h5>
+  <h5 id="objectPropertyreferences">Object Property "references"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> variant datatype property</div>
-  <div><i>Comment:</i> A datatype property that is directly associated with <a href="#classVariant">Variant</a> class instances.</div>
+  <div><i>Label:</i> references</div>
+  <div><i>Comment:</i> References another entity or resource.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000631</div>
   <div></div>
   </div>
 </p>
 <p>
-  <h5 id="datatypePropertyvariationAnnotationDatatypeProperty">Datatype Property gfvo:variationAnnotationDatatypeProperty</h5>
+  <h5 id="objectPropertyrefersTo">Object Property "refersTo"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Label:</i> variation annotation datatype property</div>
-  <div><i>Comment:</i> A variation annotation datatype property is describing a datatype property of a <a href="#classVariant">Variant</a> or <a href="#classEffect">Effect</a> class instance.</div>
+  <div><i>Label:</i> refers to</div>
+  <div><i>Comment:</i> References an entity, where additional information is provided to augment the reference.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000628</div>
   <div></div>
   </div>
 </p>
+<h4>Datatype Properties</h4>
 <p>
-  <h5 id="datatypePropertyvcfVersion">Datatype Property gfvo:vcfVersion</h5>
+  <h5 id="datatypePropertyhasValue">Datatype Property "hasValue"</h5>
   <div style="margin-left: 16px; margin-bottom: 16px">
-  <div><i>Domain:</i> <a href="#classFile">File</a></div>
-  <div><i>Range:</i> <a href="http://www.w3.org/2001/XMLSchema#float">http://www.w3.org/2001/XMLSchema#float</a></div>
-  <div>The data range has restrictions imposed on it. Please refer to the <a href="http://www.biointerchange.org/gfvo">OWL file</a> for further details.</div>
-  <div><i>Label:</i> vcf version</div>
-  <div><i>Comment:</i> Version of the VCF specification that defines the contents captured by the <a href="#classFile">File</a> class instance. The version number should be greater or equal than 4.0, but less than 5.0.</div>
-  <div><span style="margin-right: 4px;" class="badge badge-warning">VCF</span></div>
+  <div><i>Label:</i> has value</div>
+  <div><i>Comment:</i> Representation of any literal that is associated with a GFVO class instance. Domain restrictions might apply. For example, <a href="#classCodonSequence">Codon Sequence</a> entities restrict <a href="#datatypePropertyhasValue">has value</a> to be a non-empty string consisting of A, C, G, or T letters, and whose length is a multiple of 3.</div>
+  <div><i>Semanticscience Integrated Ontology property equivalence:</i> SIO_000300</div>
+  <div><span style="margin-right: 4px;" class="badge alert-danger">GFF3</span><span style="margin-right: 4px;" class="badge alert-info">GTF</span><span style="margin-right: 4px;" class="badge alert-success">GVF</span><span style="margin-right: 4px;" class="badge alert-warning">VCF</span></div>
   </div>
 </p>
 <!-- SNIP -->
@@ -1593,7 +1737,7 @@
       <hr>
 
       <footer>
-        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2013</p>
+        <p>&copy; <a href="about.html">The BioInterchange Contributors</a> 2012&ndash;2014</p>
       </footer>
 
     </div> <!-- /container -->