Update git

SEM-DISNET Documentation/index-en.html

@@ -87,13 +87,13 @@
    <div id="introduction"><h2 id="intro" class="list">Introduction <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
       <span class="markdown">
 SEM-DISNET ontology provides a integrated ontology used to describe the defined entities
-   which appear in the DISNET database. It is an ontology aimed at facilitating the analysis
+   which appear in the <a href="https://disnet.ctb.upm.es/">DISNET</a> database. It is an ontology aimed at facilitating the analysis
    of biomedical data, allowing the discovery of new patterns and associations between genes,
    drugs and their targets to be applied in cases of drug repositioning.
 
-   This project has been carried out within the DISNET project of MEDAL Laboratory (Medical
-   Data Analytics) at the CTB-UPM, together with DRUGS4COVID, developed by the OEG-UPM (Ontology
-   Engineering Group).
+   This project has been carried out within the DISNET project of <a href="https://medal.ctb.upm.es/">MEDAL Laboratory (Medical
+   Data Analytics)</a> at the <a href="http://www.ctb.upm.es/">CTB-UPM</a>, together with <a href="https://drugs4covid.oeg.fi.upm.es/">DRUGS4COVID</a>,
+   developed by the <a href="https://oeg.fi.upm.es/">OEG-UPM (Ontology Engineering Group)</a>.
 </span>
 <div id="namespacedeclarations">
 <h3 id="ns" class="list">Namespace declarations</h3>
@@ -539,13 +539,18 @@ This ontology has the following classes and properties.</span>
       This diagram follows the <a href="https://chowlk.linkeddata.es/">Chowlk notation</a>.</p>
 
       <center>
-         <img src="SEM-DISNET.jpg" alt="General overview of the SEM-DISNET Ontology." width="90%"> <figcaption><b>Figure 1</b> - SEM-DISNET schema for the representation of DISNET data.</figcaption>
+         <img src="SEM-DISNET_ontology.png" alt="General overview of the SEM-DISNET Ontology." width="90%"> <figcaption><b>Figure 1</b> - SEM-DISNET schema for the representation of DISNET data.</figcaption>
       </center>
 
       <p>  SEM-DISNET Ontology is built mostly from the reuse of existing ontology concepts. Mainly, it is based on the
-         ontology developed by DisGeNET (DisGeNET-RDF), one of the main sources used by DISNET. Other important reused
-         concepts or Classes were taken from National Cancer Institute thesaurus (NCIT), Semanticscience Integrated Ontology (SIO),
-         CHEMBL, SNOMED, Comparative Toxicogenomics Database (CTD), Orphanet Rare Disease Ontology (ORDO) and WikiPathways.
+         ontology developed by <a href="http://rdf.disgenet.org/download/v7.0.0/">DisGeNET (DisGeNET-RDF)</a>, one of the main sources used by DISNET. Other important reused
+         concepts or Classes were taken from <a href="https://github.com/NCI-Thesaurus/thesaurus-obo-edition">National Cancer Institute thesaurus (NCIT)</a>,
+         <a href="https://github.com/MaastrichtU-IDS/semanticscience/blob/master/ontology/sio.owl">Semanticscience Integrated Ontology (SIO)</a>,
+         <a href="https://github.com/chembl/GLaDOS-docs/blob/master/web-services/chembl-data-web-services.md">CHEMBL</a>,
+         <a href="https://browser.ihtsdotools.org/?perspective=full&conceptId1=404684003&edition=MAIN/2022-05-31&release=&languages=en">SNOMED</a>,
+         <a href="https://download.bio2rdf.org/files/current/ctd/ctd.html">Comparative Toxicogenomics Database (CTD)</a>,
+         <a href="https://github.com/Orphanet/ORDO">Orphanet Rare Disease Ontology (ORDO)</a> and
+         <a href="https://github.com/wikipathways/WpVocabularies/tree/master/OWL">WikiPathways</a>.
          It also reuses Object Propeties from NCIT and SIO ontologies.</p>
 
       <p> The ontology schema is organized around the central classes <tt>Disease</tt> and <tt>Drug</tt>.
@@ -649,7 +654,7 @@ This ontology has the following classes and properties.</span>
       </ul>
       </li></p>
       </p>
-      <p>The classes corresponding to the associations between concepts were incorporated into a class hierarchy, represented as
+      <p>The classes corresponding to the associations between concepts (Figure 2A) were incorporated into a class hierarchy, represented as
          a tree independently of the main diagram for the sake of clarity, since hierarchical relationships facilitates data integration.
       All Association classes represented in the diagram are subclasses of the central SIO class <tt>sio:Association</tt>.</p>
 
@@ -657,7 +662,7 @@ This ontology has the following classes and properties.</span>
          association between a drug and a target suits better with ChEMBL's <tt>ChEMBL Mechanism Class</tt>. The strategy consisted in
          creating a new DISNET class <tt>Drug Target Association</tt>, classified as a subclass of ChEMBL and SIO.</p>
 
-      <p>In the case of the Object Properties, the objective was to make the relationships between the entities as homogeneous
+      <p>In the case of the Object Properties (Figure 2B), the objective was to make the relationships between the entities as homogeneous
          as possible, so, as far as possible, an attempt was made to reuse the Object Properties of SIO or, in default, NCIT.
          However, in cases where an Object Property was not found in these ontologies with the meaning given by DISNET, an
          Object Property was created <i>de novo</i> under DISNET's namespace and classified as a subclass of the relation of
@@ -671,6 +676,9 @@ This ontology has the following classes and properties.</span>
          and classified as subclasses of those of ChEMBL and SNOMED and of <tt>sio:'is referred to by'</tt>.</p>
    </div>
 
+   <center>
+      <img src="SEM-DISNET_hierarchy.png" alt="General overview of the SEM-DISNET Ontology Class and object properties hierarchy" width="90%"> <figcaption><b>Figure 2</b> - SEM-DISNET hierarchies for Association Classes (A) and Object Properties (B).</figcaption>
+   </center>
 
 
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