upgraded to new widoco version fixing some html errors

web/2017-10-10/provenance/provenance-en.html

@@ -17,6 +17,6 @@ <h1>Provenance for COMODI: An ontology to characterise differences in versions o
 <li>The ontology documentation was the result of using the <a href="https://github.com/dgarijo/Widoco">Widoco tool</a> (which itself uses <a href="http://www.essepuntato.it/lode/">LODE</a> for generating the crossreference section).</li>
 <li>The documentation was generated at 2017-10-10</ul>
 </div>
-<p>Back to <a href="..\index-en.html">documentation</a>. <a href="provenance-en.ttl">TTL format</a></p></div>
+<p>back to <a href="..\index-en.html">documentation</a>. <a href="provenance-en.ttl">TTL format</a></p></div>
 </body> 
 </html>

web/2017-10-10/resources/extra.css

@@ -59,7 +59,7 @@ h1 {
 h3 {
     margin-top: 3px;
     padding-bottom: 5px;
-    border-bottom: 1px solid navy;
+	border-bottom: 1px solid navy;
 }
 
 h2 {

web/2017-10-10/resources/primer.css

@@ -49,4 +49,55 @@ div.fssyntax pre, div.rdfxml pre, div.owlxml pre, div.turtle pre, div.manchester
   clear: both;
   margin-left: 0em;
 }
-/* (further styles directly embedded in header template) */
+/* Expansion to add the status*/
+.status {
+    position: fixed;
+    left: 0em;
+    top: 0em;
+    text-align: right;
+    vertical-align: middle;
+    /* Square version of the inside span. Slightly larger */
+    width: 26em;
+    height: 26em;
+    z-index: -1;
+    opacity: 0.8;
+
+    /** From http://stackoverflow.com/questions/1080792/how-to-draw-vertical-text-with-css-cross-browser */
+
+    -webkit-transform: rotate(-90deg);
+    -moz-transform: rotate(-90deg);
+    -ms-transform: rotate(-90deg);
+    -o-transform: rotate(-90deg);
+    transform: rotate(-90deg);
+    /* also accepts left, right, top, bottom coordinates; not
+    * required, but a good idea for styling */
+    -webkit-transform-origin: 50% 50%;
+    -moz-transform-origin: 50% 50%;
+    -ms-transform-origin: 50% 50%;
+    -o-transform-origin: 50% 50%;
+    transform-origin: 50% 50%;
+
+    /* Should be unset in IE9+ I think. */
+    filter: progid:DXImageTransform.Microsoft.BasicImage(rotation=3);
+}
+
+/* The actual status box */
+ .status div {   
+    display: block;
+    background: rgb(0, 90, 156);
+    color: white;
+    width: 24em;
+    padding-top: 0.3em;
+    padding-left: 0em;
+    padding-right: 5em;
+    padding-bottom: 0.3em;
+    /* Enable for debugging 
+    border: red thin solid;
+     */
+} 
+
+/* And text inside, don't confuse fonts as it breaks em above */
+.status div span {
+    font-family: "Tauri";
+    font-size: larger;
+}

web/2017-10-10/resources/rec.css

@@ -16,6 +16,7 @@ body {
   background-position: top left;
   background-attachment: fixed;
   background-repeat: no-repeat;
+  counter-reset:section;
 }
 :link { color: #00C; background: transparent }
 :visited { color: #609; background: transparent }
@@ -33,6 +34,12 @@ th, td { /* ns 4 */
 }
 
 h1, h2, h3, h4, h5, h6 { text-align: left }
+h2.list{counter-reset:subsection }
+h2.list:before{counter-increment:section;content: counter(section) ". ";}
+h3.list:before{counter-increment:subsection;content: counter(section) "." counter(subsection) ". ";
+	}
+h3.list{margin-top: 20px;
+	border-bottom: 0px; }
 /* background should be transparent, but WebTV has a bug */
 h1, h2, h3 { color: #005A9C; background: white }
 h1 { font: 170% sans-serif }

web/2017-10-10/sections/abstract-en.html

@@ -7,9 +7,7 @@ <h2>Abstract</h2>
 </p>
 <p>
 <strong>The OWL encoding</strong> of the COMODI Ontology is available from our web server: <a href="comodi.owl">comodi.owl</a>.<br />
-<strong>The namespace</strong> for all COMODI terms is <code>http://purl.uni-rostock.de/comodi/comodi#</code>.<br /> 
-<strong>Please cite COMODI as:</strong>
-Martin Scharm, Dagmar Waltemath, Pedro Mendes, and Olaf Wolkenhauer (2016): <strong>COMODI: an ontology to characterise differences in versions of computational models in biology.</strong> <em>Journal of Biomedical Semantics</em> 2016; 7:46; <a href="https://dx.doi.org/10.1186/s13326-016-0080-2">https://dx.doi.org/10.1186/s13326-016-0080-2</a><br />
+<strong>The namespace</strong> for all COMODI terms is <code>http://purl.uni-rostock.de/comodi/comodi#</code>.
 </p>
 
 

web/2017-10-10/sections/acknowledgements-en.html

@@ -0,0 +1,13 @@
+
+<h2 class="list" id="ack">Acknowledgements <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
+<p>The authors would like to thank 
+the <a href="http://co.mbine.org/">COMBINE community</a> and the participants of the <a href="http://icsb15.apbionet.org/">2015 ICSB</a> for valuable discussions and their expertise that significantly improved the outcome of this work.
+</p>
+
+<p>
+Further to this, the authors would like to thank <a href="http://palindrom.es/phd/whoami/">Silvio Peroni</a> for developing <a href="http://www.essepuntato.it/lode">LODE</a>, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and <a href="http://delicias.dia.fi.upm.es/members/dgarijo/">Daniel Garijo</a> for developing the Java tool <a href="https://github.com/dgarijo/Widoco">widoco</a>, which was used to generate this website, and the <a href="http://protege.stanford.edu/about.php">Protege team</a> for providing <a href="http://protege.stanford.edu/">Protege</a>, the software tool we used to build the ontology.
+</p>
+
+<p> This work was funded by the German Federal Ministry of Education and
+Research (<a href="https://www.bmbf.de/">BMBF</a>) as part of the e:Bio program <a href="https://sems.uni-rostock.de/">SEMS</a>, FKZ 031 6194.
+</p>