Fixed descriptions about GFVO (no more mention of GFF30 and GVF30). A…

…dded reference to CC0.

web/ontologies.html

@@ -54,10 +54,10 @@ <h2>Overview</h2>
               <li><a href="http://code.google.com/p/semanticscience/wiki/SIO">Semanticscience Integrated Ontology</a> (SIO)</li>
             </ul>
           </p>
-          <p>One particular ontology &mdash; the Genomic Feature and Variation Ontology &mdash; that we will be using in the next release of BioInterchange for converting <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, and <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF</a> file formats into RDF is described below. The current version of BioInterchange makes use of <a href="https://github.com/BioInterchange/Ontologies">GFF3O</a> and <a href="https://github.com/BioInterchange/Ontologies">GVF1O</a>, which were merged into GFVO.
-          <p>The <b>BioInterchange vocabulary wrappers</b> that are available for Ruby, Python and Java, are described as part of the <a href="api.html">API</a> documentation.</p>
+          <p>One particular ontology &mdash; the Genomic Feature and Variation Ontology &mdash; is being used for converting <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, and <a href="http://samtools.github.io/hts-specs/VCFv4.2.pdf">VCF</a> file formats into RDF as described below.
           <h2>Genomic Feature and Variation Ontology (GFVO)</h2>
-          <p>The Genomic Feature and Variation Ontology (GFVO) enables the RDFization of genomic feature and variation data. It particularly addresses the representation of data in <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, and <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF</a> formats (the latter two representation are still in development).</p>
+          <p>The Genomic Feature and Variation Ontology (GFVO) enables the RDFization of genomic feature and variation data. It particularly addresses the representation of data in <a href="http://www.sequenceontology.org/resources/gff3.html">GFF3</a>, <a href="http://www.sequenceontology.org/resources/gvf.html">GVF</a>, <a href="http://www.ensembl.org/info/website/upload/gff.html">GTF</a>, and <a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41">VCF</a> formats.</p>
+          <p>The ontology is available under the <a href="http://creativecommons.org/publicdomain/zero/1.0/">CC0 1.0 Universal</a> license, and therefore, de-facto within the public domain.</p>
           <p>GFVO can be loaded into <a href="http://protege.stanford.edu">Prot&eacute;g&eacute;</a> or <a href="http://www.topquadrant.com/products/TB_Composer.html">TopBraid Composer</a> via: <a href="http://www.biointerchange.org/gfvo">http://www.biointerchange.org/gfvo</a></p>
           <ol>
             <li><a href="#external">External Ontologies and Linked Data</a></li>
@@ -70,8 +70,8 @@ <h2>Genomic Feature and Variation Ontology (GFVO)</h2>
             </ol>
           </ol>
           <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>
+          <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://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>, 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="https://www.linkedin.com/in/takatomofujisawa">Takatomo Fujisawa</a>, <a href="http://www.linkedin.com/in/toshiakikatayama">Toshiaki Katayama</a>, <a href="http://berkeleybop.org/person/chris-mungall">Chris Mungall</a>, and <a href="http://www.linkedin.com/in/francescostrozzi">Francesco Strozzi</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>