Edited the landing page, readme; removed redirects.

BioPAX · Jun 19, 2024 · a66d0ee · a66d0ee
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diff --git a/.gitignore b/.gitignore
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+/.idea
+
diff --git a/README.md b/README.md
@@ -1,39 +1,5 @@
-# BioPAX.org
-(http://biopax.github.io)
+# BioPAX GitHub organization website
 
-Biological Pathways Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in [OWL DL](http://www.w3.org/TR/owl-features/) and is represented in the RDF/XML format. [BioPAX Paper](http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html) was published in Nature Biotechnology in 2010.
+See the result page at https://biopax.github.io but better go to www.biopax.org
 
-## "Hello World" example:
-```
-<?xml version="1.0" encoding="UTF-8"?>
-<rdf:RDF
- xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
- xmlns:owl="http://www.w3.org/2002/07/owl#"
- xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
- xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base="">
-<owl:Ontology rdf:about="">
- <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
-</owl:Ontology>
-  <bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld">
-    <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello World!</bp:displayName>
-  </bp:Protein>
-</rdf:RDF>
-```
-
-## Links:
-* BioPAX ontology and documentation [releases](http://www.biopax.org/release/)
-* BioPAX ontology [visualization](http://vowl.visualdataweb.org/webvowl/#iri=http://www.biopax.org/release/biopax-level3.owl) using WebVOWL (cool!)
-* BioPAX secification [sub-project](https://github.com/BioPAX/specification)
-* BioPAX model [examples](https://github.com/BioPAX/specification/blob/master/Level3/examples/)
-* BioPAX [archive and downloads](http://www.biopax.org/downloads/biopax/)
-
-## PS:
-
-Official BioPAX web site www.biopax.org has been at CBIO MSKCC until 2013; 
-then it was moved to Sourceforge (Project-Web hosting, FRS, biopax.sf.net). 
-Now, we are migrating from Sourceforge.
-
-
-Sincerely yours,
-
-BioPAX team.
+The [BioPAX Paper](http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html) 
diff --git a/_config.yml b/_config.yml
@@ -1,3 +1,2 @@
-gems:
-  - jekyll-redirect-from
-
+#gems:
+#  - jekyll-redirect-from
diff --git a/biopax-validator.md b/biopax-validator.md
diff --git a/downloads.md b/downloads.md
diff --git a/index.html b/index.html
@@ -8,12 +8,7 @@
     <link rel="stylesheet" type="text/css" href="stylesheets/stylesheet.css" media="screen">
     <link rel="stylesheet" type="text/css" href="stylesheets/github-light.css" media="screen">
     <link rel="stylesheet" type="text/css" href="stylesheets/print.css" media="print">
-
-    <!--[if lt IE 9]>
-    <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
-    <![endif]-->
-
-    <title>BioPAX (on Github)</title>
+    <title>BioPAX</title>
   </head>
 
   <body>
@@ -29,32 +24,32 @@ <h2>Biological Pathway Exchange</h2>
       <div class="inner clearfix">
         <section id="main-content">
 
-          <p>Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis 
-          of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity 
-          of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort 
-          by the community of researchers, software developers, and institutions. BioPAX is defined in 
-          <a href="http://www.w3.org/TR/owl-features/">OWL DL</a> and is represented in the RDF/XML format. For more details, see 
-          <a href="http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html">Demir E <em>et al.</em> 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9)</a>.
-          </p>          
-          
+          <p>Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis
+          of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity
+          of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort
+          by the community of researchers, software developers, and institutions. BioPAX is defined in
+          <a href="https://www.w3.org/TR/owl-features/">OWL DL</a> and is represented in the RDF/XML format. For more details, see
+          <a href="https://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html">Demir E <em>et al.</em> 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9)</a>.
+          </p>
+
           <h2><a id="links" class="anchor" href="#links" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link">
           </span></a>Links:</h2>
 
           <ul>
-            <li>BioPAX ontology and documentation <a href="http://www.biopax.org/release/">releases</a></li>
-            <li>Specification <a href="https://github.com/BioPAX/specification">development</a></li>            
-            <li><a href="http://www.biopax.org/downloads/biopax/">Archive and downloads</a></li>
+            <li>BioPAX ontology and documentation <a href="https://www.biopax.org/release/">releases</a></li>
+            <li>Specification <a href="https://github.com/BioPAX/specification/">development</a></li>
+            <li><a href="https://www.biopax.org/downloads/biopax/">Archive and downloads</a></li>
             <li><a href="https://groups.google.com/forum/#!forum/biopax-discuss">Google group</a></li>
-            <li><a href="http://www.biopax.org/mediawiki">Wiki (archive)</a></li>
-            <li><a href="http://www.biopax.org/validator">BioPAX validator</a></li>
-            <li><a href="http://co.mbine.org/standards/biopax">BioPAX @ COMBINE</a></li>
-            <li>View BioPAX via  
+            <li><a href="https://www.biopax.org/wiki/">Wiki (archive)</a></li>
+            <li><a href="https://www.biopax.org/validator/">BioPAX validator</a></li>
+            <li><a href="https://co.mbine.org/standards/">BioPAX @ COMBINE</a></li>
+            <li>View BioPAX via
                 <ul>
                   <li><a href="https://webprotege.stanford.edu/#projects/0047e89b-3018-4a7e-a725-ff78e3f497bb">WebProtege</a>(requires an account)</li>
-                  <li><a href="http://www.biopax.org/owldoc/Level3/">OWLdoc</a></li>
-                  <li><a href="http://vowl.visualdataweb.org/webvowl/#iri=http://www.biopax.org/release/biopax-level3.owl">WebVOWL</a></li>                    
+                  <li><a href="https://www.biopax.org/owldoc/Level3/">OWLdoc</a></li>
+                  <li><a href="https://vowl.visualdataweb.org/webvowl/#iri=http://www.biopax.org/release/biopax-level3.owl">WebVOWL</a></li>
                 </ul>
-              </li>  
+              </li>
           </ul>
 
           <h2>
@@ -63,37 +58,37 @@ <h2>
           </h2>
 
           <pre><code>&lt;?xml version="1.0" encoding="UTF-8"?&gt;
-          &lt;rdf:RDF
-          xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-          xmlns:owl="http://www.w3.org/2002/07/owl#"
-          xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-          xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base=""&gt;
-          &lt;owl:Ontology rdf:about=""&gt;
-          &lt;owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" /&gt;
-          &lt;/owl:Ontology&gt;
-            &lt;bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld"&gt;
-              &lt;bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"&gt;Hello World!&lt;/bp:displayName&gt;
-            &lt;/bp:Protein&gt;
-          &lt;/rdf:RDF&gt;
+&lt;rdf:RDF
+xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+xmlns:owl="http://www.w3.org/2002/07/owl#"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base=""&gt;
+&lt;owl:Ontology rdf:about=""&gt;
+&lt;owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" /&gt;
+&lt;/owl:Ontology&gt;
+  &lt;bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld"&gt;
+    &lt;bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string"&gt;Hello World!&lt;/bp:displayName&gt;
+  &lt;/bp:Protein&gt;
+&lt;/rdf:RDF&gt;
           </code></pre>
 
           <p>More examples <a href="https://github.com/BioPAX/specification/blob/master/Level3/examples/">examples</a><p></p>
-           
+
           <h2>Scientific Advisory Board</h2>
           <p>
-          <li><a href="http://baderlab.org/GaryBader">Gary Bader</a>, University of Toronto</li>
-          <li><a href="http://www.med.nyu.edu/people/P.DEustachio.html">Peter D'Eustachio</a>, New York University</li>
-          <li><a href="http://www.ebi.ac.uk/~hhe/">Henning Hermjakob</a>, European Bioinformatics Institute</li>
-          <li><a href="http://www.ebi.ac.uk/compneur-srv/">Nicolas LeNovere</a>, European Bioinformatics Institute</li>
-          <li><a href="http://www.ai.sri.com/pkarp/">Peter Karp</a>, SRI International</li>
-          <li><a href="http://sanderlab.org/">Chris Sander</a> Harvard University</li>
-          </p>                 
+          <li><a href="https://baderlab.org/GaryBader">Gary Bader</a>, University of Toronto</li>
+          <li><a href="https://med.nyu.edu/faculty/peter-g-d-eustachio">Peter D'Eustachio</a>, New York University</li>
+          <li><a href="https://www.ebi.ac.uk/people/person/henning-hermjakob/">Henning Hermjakob</a>, European Bioinformatics Institute</li>
+          <li><a href="https://www.ebi.ac.uk/compneur-srv/">Nicolas LeNovere</a>, European Bioinformatics Institute</li>
+          <li><a href="https://www.ai.sri.com/pkarp/">Peter Karp</a>, SRI International</li>
+          <li><a href="https://www.sanderlab.org/">Chris Sander</a> Harvard University</li>
+          </p>
+        </section>
 
-         </section>
         <aside id="sidebar">
-          <p>This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the Architect theme by <a href="https://twitter.com/jasonlong">Jason Long</a>.</p>
+          <p>This page was generated by <a href="https://pages.github.com">GitHub Pages</a>
+            using the Architect theme by <a href="https://twitter.com/jasonlong">Jason Long</a>.</p>
         </aside>
-
       </div>
     </div>
 
@@ -104,7 +99,7 @@ <h2>Scientific Advisory Board</h2>
     <script type="text/javascript">
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         var pageTracker = _gat._getTracker("UA-43341809-1");
-      pageTracker._trackPageview();
+        pageTracker._trackPageview();
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diff --git a/m2repo.md b/m2repo.md
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