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definitions/mapping/index.html

@@ -818,7 +818,7 @@ <h3 id="mapping-definition-file_1">Mapping definition File<a class="headerlink"
 <p>The file must have <strong><em>5 columns</em></strong> with headers defined as follows:</p>
 <ul>
 <li>column 1 - <strong>CVname</strong> : name of the mapping entry</li>
-<li>column 2 - <strong>CVtype</strong> : type of the CV target (must be either <em>bioportal</em> or <em>skosmos</em>)</li>
+<li>column 2 - <strong>CVtype</strong> : type of the CV target (by default, must be either <em>ontoportal</em>, <em>skosmos</em> or <em>ols</em>)</li>
 <li>column 3 - <strong>CVurl</strong> : URL of the corresponding web API</li>
 <li>column 4 - <strong>CVterm</strong> : name of the thesaurus or the ontology list separated by a comma</li>
 <li>column 5 - <strong>CVlang</strong> : the chosen language (mainly for thesauri)</li>

definitions/vocabulary/index.html

@@ -847,25 +847,44 @@ <h3 id="vocabulary_1">Vocabulary<a class="headerlink" href="#vocabulary_1" title
 <a href="../../images/vocabulary_fig4.png" data-lightbox="fig4"><img src="../../images/vocabulary_fig4.png" width="800px"></a>
 </center>
 <br></p>
-<p><strong>5</strong> - <strong>Vocabulary based on a SKOSMOS Thesaurus with multiple selection</strong> (<em>multiselect</em>) </p>
+<p><strong>5</strong> - <strong>Multi-select vocabulary, based on an <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> managed by Twitter's Typeahead library.</strong> (<em>multiselect</em>) </p>
 <ul>
-<li><a href="https://skosmos.org/" target="_blank">SKOSMOS</a> is a web tool facilitating the posting of controlled vocabulary online in the form of a <a href="https://en.wikipedia.org/wiki/Thesaurus_(information_retrieval)" target="_blank">thesaurus</a> according to the <a href="https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System" target="_blank">SKOS</a> data model. It offers a navigation interface as well as a web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. A simple JavaScript allows you to easily connect this web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> with a multiselect field.</li>
-<li>The JavaScript file must have the same name as the assigned variable (here <em>VOvocab</em>) and must present under <em>web/js/autocomplete</em>. See for instance <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/autocomplete/VOvocab.js" target="_blank">VOvocab.js</a>.</li>
+<li>Maggot embeds <a href="https://twitter.github.io/typeahead.js/" target="_blank">Twitter's Typeahead library</a> making it relatively easy for a data manager to implement a new vocabulary from its web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. To do this, it is necessary to create two scripts (<em>&lt;ws&gt;_typeahead.js</em> and <em>&lt;wstype&gt;.inc</em>) which will each be used at one stage of the process as shown in the following figure:</li>
 </ul>
 <p><center>
-<a href="https://thesaurus.inrae.fr/thesaurus-inrae/en/" target="_blank"><img src="../../images/vocabulary_fig5.png" width="800px"></a>
+<a href="../../images/vocabulary_fig7.png" data-lightbox="fig7"><img src="../../images/vocabulary_fig7.png" width="600px"></a>
 </center>
 <br></p>
-<p><strong>6</strong> - <strong>Vocabulary based on an OntoPortal with multiple selection</strong> (<em>multiselect</em>) </p>
 <ul>
-<li>Portals based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> offer the wealth of ontologies according to several domains of application (e.g. <a href="https://bioportal.bioontology.org/" target="_blank">BioPortal</a> in the biomedical domain, <a href="https://agroportal.lirmm.fr/" target="_blank">AgroPortal</a> in the domain of plants).</li>
-<li>No need of JavaScript file. The <a href="https://bioportal.bioontology.org/ontologies/STY?p=widgets" target="_blank">Bioportal Autocompletion widget</a> has been <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/bpsearch.min.js" target="_blank">implemented into Maggot</a>. You have to only declare the ontology you want to use directly into the terminology definition file in order to easily connect this widget with a multiselect field.</li>
+<li>
+<p><em>&lt;ws&gt;_typeahead.js</em> : This file corresponds to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> call when entering vocabulary using Twitter's Typeahead library. The prefix <em>&lt;ws&gt;</em> standing for web service, must be positioned so as to correspond to the name of the service indicated in the <em>CVname</em> column of the mapping file (<a href="../mapping"><em>web/conf/mapping.txt</em></a>) as well as to the corresponding value for the '<em>ws</em>' attribute in the column '<em>features</em>' of the terminology definition file (see <a href="../terminology">definitions</a>). This file must then be placed under the <em>web/js/autocomplete</em> directory. You will find a <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/autocomplete/template_typeahead.js" target="_blank">template file</a> in this directory.</p>
+</li>
+<li>
+<p><em>&lt;wstype&gt;.inc</em> : This file corresponds to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> call while metadata crosswalks processus and based on the mapping file (<a href="../mapping"><em>web/conf/mapping.txt</em></a>).The prefix <em>&lt;ws_type&gt;</em> standing for web service type, must be positioned so as to correspond to the type of the service indicated in the <em>CVtype</em> column of the mapping file. This file must then be placed under the <em>web/inc/mapping/</em> directory. You will find a <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/mapping/template.inc" target="_blank">template file</a> in this directory.</p>
+</li>
+<li>
+<p>With the help of this library, this allows you to select a term from a list of vocabulary terms within a drop-down list. The list of terms has been pre-selected based on the first letters entered in the “Search for value” box. This list is dynamically refreshed when letters are added or modified. So, unlike a single call to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> returning the entire list of terms in memory, which can take a very long time to load, the calls are made dynamically on the basis of a portion of a word, thus limiting the number of terms to retrieve. Thus this makes use very fluid.</p>
+</li>
+<li>
+<p>By defaut, Maggot already provides some vocaburay web services implemented in this way such as The <a href="https://skosmos.org/" target="_blank">SKOSMOS</a> thesauri, the ontology portals based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> and the <a href="https://www.ebi.ac.uk/ols4" target="_blank">EMBL-EBI Ontology Lookup Service</a> (OLS) The figure shows the configuration in the terminology definition file and the corresponding screenshots for each vocabulary.</p>
+</li>
 </ul>
 <p><center>
-<a href="https://agroportal.lirmm.fr/" target="_blank"><img src="../../images/vocabulary_fig6.png" width="800px"></a>
+<a href="../../images/vocabulary_fig7b.png" data-lightbox="fig7b"><img src="../../images/vocabulary_fig7b.png" width="800px"></a>
 </center>
 <br></p>
-<p><br></p>
+<ul>
+<li>
+<p><a href="https://skosmos.org/" target="_blank">SKOSMOS</a> is a web tool facilitating the posting of controlled vocabulary online in the form of a <a href="https://en.wikipedia.org/wiki/Thesaurus_(information_retrieval)" target="_blank">thesaurus</a> according to the <a href="https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System" target="_blank">SKOS</a> data model. It offers a navigation interface as well as a web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. See for example the <a href="https://thesaurus.inrae.fr/thesaurus-inrae/en/" target="_blank">VOINRAE thesaurus</a></p>
+</li>
+<li>
+<p><a href="https://agroportal.lirmm.fr/" target="_blank">AgroPortal</a> and <a href="https://bioportal.bioontology.org/" target="_blank">BioPortal</a> are both based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> which is a generic technology to build ontology repositories or semantic artefact catalogues.</p>
+</li>
+<li>
+<p><a href="https://www.ebi.ac.uk/ols4" target="_blank">EMBL-EBI Ontology Lookup Service</a> is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. You can browse the ontologies through the website as well as programmatically via the OLS <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. 
+<br></p>
+</li>
+</ul>
 
 
 

print_page/index.html

@@ -1381,25 +1381,44 @@ <h3 id="definitions-vocabulary-vocabulary_1">Vocabulary<a class="headerlink" hre
 <a href="../images/vocabulary_fig4.png" data-lightbox="fig4"><img src="../images/vocabulary_fig4.png" width="800px"></a>
 </center>
 <br></p>
-<p><strong>5</strong> - <strong>Vocabulary based on a SKOSMOS Thesaurus with multiple selection</strong> (<em>multiselect</em>) </p>
+<p><strong>5</strong> - <strong>Multi-select vocabulary, based on an <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> managed by Twitter's Typeahead library.</strong> (<em>multiselect</em>) </p>
 <ul>
-<li><a href="https://skosmos.org/" target="_blank">SKOSMOS</a> is a web tool facilitating the posting of controlled vocabulary online in the form of a <a href="https://en.wikipedia.org/wiki/Thesaurus_(information_retrieval)" target="_blank">thesaurus</a> according to the <a href="https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System" target="_blank">SKOS</a> data model. It offers a navigation interface as well as a web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. A simple JavaScript allows you to easily connect this web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> with a multiselect field.</li>
-<li>The JavaScript file must have the same name as the assigned variable (here <em>VOvocab</em>) and must present under <em>web/js/autocomplete</em>. See for instance <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/autocomplete/VOvocab.js" target="_blank">VOvocab.js</a>.</li>
+<li>Maggot embeds <a href="https://twitter.github.io/typeahead.js/" target="_blank">Twitter's Typeahead library</a> making it relatively easy for a data manager to implement a new vocabulary from its web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. To do this, it is necessary to create two scripts (<em>&lt;ws&gt;_typeahead.js</em> and <em>&lt;wstype&gt;.inc</em>) which will each be used at one stage of the process as shown in the following figure:</li>
 </ul>
 <p><center>
-<a href="https://thesaurus.inrae.fr/thesaurus-inrae/en/" target="_blank"><img src="../images/vocabulary_fig5.png" width="800px"></a>
+<a href="../images/vocabulary_fig7.png" data-lightbox="fig7"><img src="../images/vocabulary_fig7.png" width="600px"></a>
 </center>
 <br></p>
-<p><strong>6</strong> - <strong>Vocabulary based on an OntoPortal with multiple selection</strong> (<em>multiselect</em>) </p>
 <ul>
-<li>Portals based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> offer the wealth of ontologies according to several domains of application (e.g. <a href="https://bioportal.bioontology.org/" target="_blank">BioPortal</a> in the biomedical domain, <a href="https://agroportal.lirmm.fr/" target="_blank">AgroPortal</a> in the domain of plants).</li>
-<li>No need of JavaScript file. The <a href="https://bioportal.bioontology.org/ontologies/STY?p=widgets" target="_blank">Bioportal Autocompletion widget</a> has been <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/bpsearch.min.js" target="_blank">implemented into Maggot</a>. You have to only declare the ontology you want to use directly into the terminology definition file in order to easily connect this widget with a multiselect field.</li>
+<li>
+<p><em>&lt;ws&gt;_typeahead.js</em> : This file corresponds to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> call when entering vocabulary using Twitter's Typeahead library. The prefix <em>&lt;ws&gt;</em> standing for web service, must be positioned so as to correspond to the name of the service indicated in the <em>CVname</em> column of the mapping file (<a href="#definitions-mapping"><em>web/conf/mapping.txt</em></a>) as well as to the corresponding value for the '<em>ws</em>' attribute in the column '<em>features</em>' of the terminology definition file (see <a href="#definitions-terminology">definitions</a>). This file must then be placed under the <em>web/js/autocomplete</em> directory. You will find a <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/js/autocomplete/template_typeahead.js" target="_blank">template file</a> in this directory.</p>
+</li>
+<li>
+<p><em>&lt;wstype&gt;.inc</em> : This file corresponds to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> call while metadata crosswalks processus and based on the mapping file (<a href="#definitions-mapping"><em>web/conf/mapping.txt</em></a>).The prefix <em>&lt;ws_type&gt;</em> standing for web service type, must be positioned so as to correspond to the type of the service indicated in the <em>CVtype</em> column of the mapping file. This file must then be placed under the <em>web/inc/mapping/</em> directory. You will find a <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/mapping/template.inc" target="_blank">template file</a> in this directory.</p>
+</li>
+<li>
+<p>With the help of this library, this allows you to select a term from a list of vocabulary terms within a drop-down list. The list of terms has been pre-selected based on the first letters entered in the “Search for value” box. This list is dynamically refreshed when letters are added or modified. So, unlike a single call to the <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr> returning the entire list of terms in memory, which can take a very long time to load, the calls are made dynamically on the basis of a portion of a word, thus limiting the number of terms to retrieve. Thus this makes use very fluid.</p>
+</li>
+<li>
+<p>By defaut, Maggot already provides some vocaburay web services implemented in this way such as The <a href="https://skosmos.org/" target="_blank">SKOSMOS</a> thesauri, the ontology portals based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> and the <a href="https://www.ebi.ac.uk/ols4" target="_blank">EMBL-EBI Ontology Lookup Service</a> (OLS) The figure shows the configuration in the terminology definition file and the corresponding screenshots for each vocabulary.</p>
+</li>
 </ul>
 <p><center>
-<a href="https://agroportal.lirmm.fr/" target="_blank"><img src="../images/vocabulary_fig6.png" width="800px"></a>
+<a href="../images/vocabulary_fig7b.png" data-lightbox="fig7b"><img src="../images/vocabulary_fig7b.png" width="800px"></a>
 </center>
 <br></p>
-<p><br></p></section><section class="print-page" id="definitions-mapping"><h1 id="definitions-mapping-mapping-definition-file">Mapping Definition File<a class="headerlink" href="#definitions-mapping-mapping-definition-file" title="Permanent link">&para;</a></h1>
+<ul>
+<li>
+<p><a href="https://skosmos.org/" target="_blank">SKOSMOS</a> is a web tool facilitating the posting of controlled vocabulary online in the form of a <a href="https://en.wikipedia.org/wiki/Thesaurus_(information_retrieval)" target="_blank">thesaurus</a> according to the <a href="https://en.wikipedia.org/wiki/Simple_Knowledge_Organization_System" target="_blank">SKOS</a> data model. It offers a navigation interface as well as a web <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. See for example the <a href="https://thesaurus.inrae.fr/thesaurus-inrae/en/" target="_blank">VOINRAE thesaurus</a></p>
+</li>
+<li>
+<p><a href="https://agroportal.lirmm.fr/" target="_blank">AgroPortal</a> and <a href="https://bioportal.bioontology.org/" target="_blank">BioPortal</a> are both based on <a href="https://ontoportal.org/" target="_blank">OntoPortal</a> which is a generic technology to build ontology repositories or semantic artefact catalogues.</p>
+</li>
+<li>
+<p><a href="https://www.ebi.ac.uk/ols4" target="_blank">EMBL-EBI Ontology Lookup Service</a> is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions. You can browse the ontologies through the website as well as programmatically via the OLS <abbr title="Application Program Interface in contrast with a User Interface. It is a way for two or more computer programs to communicate with each other.">API</abbr>. 
+<br></p>
+</li>
+</ul></section><section class="print-page" id="definitions-mapping"><h1 id="definitions-mapping-mapping-definition-file">Mapping Definition File<a class="headerlink" href="#definitions-mapping-mapping-definition-file" title="Permanent link">&para;</a></h1>
 <style>.md-typeset h1 {display: none;} .md-nav__item {font-size: medium}</style>
 
 <h3 id="definitions-mapping-mapping-definition-file_1">Mapping definition File<a class="headerlink" href="#definitions-mapping-mapping-definition-file_1" title="Permanent link">&para;</a></h3>
@@ -1412,7 +1431,7 @@ <h3 id="definitions-mapping-mapping-definition-file_1">Mapping definition File<a
 <p>The file must have <strong><em>5 columns</em></strong> with headers defined as follows:</p>
 <ul>
 <li>column 1 - <strong>CVname</strong> : name of the mapping entry</li>
-<li>column 2 - <strong>CVtype</strong> : type of the CV target (must be either <em>bioportal</em> or <em>skosmos</em>)</li>
+<li>column 2 - <strong>CVtype</strong> : type of the CV target (by default, must be either <em>ontoportal</em>, <em>skosmos</em> or <em>ols</em>)</li>
 <li>column 3 - <strong>CVurl</strong> : URL of the corresponding web API</li>
 <li>column 4 - <strong>CVterm</strong> : name of the thesaurus or the ontology list separated by a comma</li>
 <li>column 5 - <strong>CVlang</strong> : the chosen language (mainly for thesauri)</li>