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definitions/index.html

@@ -766,7 +766,7 @@ <h3 id="metadata-definition-files">Metadata definition files<a class="headerlink
 <p>There are <strong>two levels of definition files</strong> as shown the figure below:</p>
 <p><center><a href="../images/definitions_fig2.png" data-lightbox="fig2"><img src="../images/definitions_fig2.png" width="600px"></a></center></p>
 <p><strong>1</strong> - The first level concerns the definition of terminology (metadata) similar to a <a href="https://sustainableheritagenetwork.org/system/files/atoms/file/How_to_Create_a_Descriptive_Metadata_Plan.pdf" target="_blank">descriptive metadata plan</a>. Clearly, this category is more akin to configuration files. They represent the heart of the application around which everything else is based. The input and search interfaces are completely generated from these definition files (especially the <em><a href="terminology">web/conf/config_terms.txt</a></em> file), thus defining each of the fields, their <a href="../images/terminology_types.png" data-lightbox="fig3">input type</a> (<em>checkbox</em>, <em>dropbox</em>, <em>textbox</em>, ...) and the associated <a href="vocabulary">controlled vocabulary</a> (ontology and thesaurus by <abbr title="feature in which an application predicts the rest of a word a user is typing">autocompletion</abbr>, drop-down list according to a list of fixed terms). This is why a <a href="../configuration">configuration step</a> is essential in order to be able to configure all the other modules.</p>
-<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="dataverse">Dataverse</a>, <a href="zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (<em><a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/config/config.inc" target="_blank">web/inc/config/config.inc</a></em>).</p>
+<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="dataverse">Dataverse</a>, <a href="zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="../settings/#incconfigconfiginc">Settings</a>).</p>
 <p>All definition files are made using a simple spreadsheet then exported in <abbr title="Open text format representing tabular data as &quot;Tab-Separated Values&quot;. Each row corresponds to a table row and the cells in a row are separated by a tab">TSV</abbr> format. </p>
 <p>The list of definition files in Maggot are given below. All must be put under the directory <em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>.
 <center><a href="https://pmb-bordeaux.fr/maggot/config/view" target="_blank"><img src="../images/definitions_fig1.png" width="600px"></a></center></p>

installation/index.html

@@ -1069,7 +1069,7 @@ <h3 id="architecture-diagram">Architecture diagram<a class="headerlink" href="#a
 </center></p>
 <hr />
 <h3 id="file-browser">File Browser<a class="headerlink" href="#file-browser" title="Permanent link">&para;</a></h3>
-<p>You can provide access to your data via a <a href="https://filebrowser.org/" target="_blank">file browser</a>. This application must be <a href="https://github.com/djacob65/maggot-fb" target="_blank">installed separately</a> but can be connected to Maggot by specifying the corresponding URL in the <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/config/config.inc" target="_blank">configuration file</a>. Users and their rights are managed in the filebrowser application. Likewise, we can also <a href="../images/filebrowser_fig2.png" data-lightbox="fig2">create links to the data without a password</a>. These links can be usefully specified as external resources in the metadata managed by Maggot.</p>
+<p>You can provide access to your data via a <a href="https://filebrowser.org/" target="_blank">file browser</a>. This application must be <a href="https://github.com/djacob65/maggot-fb" target="_blank">installed separately</a> but can be connected to Maggot by specifying the corresponding URL in the <a href="../settings/#incconfigconfiginc">configuration file</a>. Users and their rights are managed in the filebrowser application. Likewise, we can also <a href="../images/filebrowser_fig2.png" data-lightbox="fig2">create links to the data without a password</a>. These links can be usefully specified as external resources in the metadata managed by Maggot.</p>
 <p><center>
 <a href="../images/filebrowser_fig1.png" data-lightbox="fig10"><img src="../images/filebrowser_fig1.png" width="800px"></a><br>
  <em>See how to do install in <a href="https://github.com/djacob65/maggot-fb" target="_blank">github</a>.</em>

print_page/index.html

@@ -890,7 +890,7 @@ <h1 class='nav-section-title' id='section-quick-tutorial'>
 
 <h3 id="tutorial-describe-metadata-entry">Metadata Entry<a class="headerlink" href="#tutorial-describe-metadata-entry" title="Permanent link">&para;</a></h3>
 <p>The figures are given here for illustration purposes but certain elements may be different for you given that this will depend on the configuration on your instance, in particular the choice of metadata, and the associated vocabulary sources.</p>
-<p>Indeed, the choice of vocabulary sources (ontologies, thesauri, dictionaries) as well as the choice of metadata fields to enter must in principle have been the subject of discussion between data producers and <abbr title="The data manager is the person who sets the data policy, i.e. its implementation and governance.">data manager</abbr> during the implementation of the Maggot tool in order to find the best compromise between the choice of sources and all the scientific fields targeted (see <a href="#definitions">Definition files</a>). However a later addition is always possible.</p>
+<p>Indeed, the choice of vocabulary sources (ontologies, thesauri, dictionaries) as well as the choice of metadata fields to enter must in principle have been the subject of discussion between <abbr title="The data producers are the people who produced data and by extension have rights over it. They are also those who have the best knowledge of it.">data producers</abbr> and <abbr title="The data manager is the person who sets the data policy, i.e. its implementation and governance.">data manager</abbr> during the implementation of the Maggot tool in order to find the best compromise between the choice of sources and all the scientific fields targeted (see <a href="#definitions">Definition files</a>). However a later addition is always possible.</p>
 <p><br></p>
 <h4 id="tutorial-describe-overview">Overview<a class="headerlink" href="#tutorial-describe-overview" title="Permanent link">&para;</a></h4>
 <p>When you enter the metadata entry module you should see a page that looks like the figure below:</p>
@@ -1219,7 +1219,7 @@ <h3 id="installation-architecture-diagram">Architecture diagram<a class="headerl
 </center></p>
 <hr />
 <h3 id="installation-file-browser">File Browser<a class="headerlink" href="#installation-file-browser" title="Permanent link">&para;</a></h3>
-<p>You can provide access to your data via a <a href="https://filebrowser.org/" target="_blank">file browser</a>. This application must be <a href="https://github.com/djacob65/maggot-fb" target="_blank">installed separately</a> but can be connected to Maggot by specifying the corresponding URL in the <a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/config/config.inc" target="_blank">configuration file</a>. Users and their rights are managed in the filebrowser application. Likewise, we can also <a href="../images/filebrowser_fig2.png" data-lightbox="fig2">create links to the data without a password</a>. These links can be usefully specified as external resources in the metadata managed by Maggot.</p>
+<p>You can provide access to your data via a <a href="https://filebrowser.org/" target="_blank">file browser</a>. This application must be <a href="https://github.com/djacob65/maggot-fb" target="_blank">installed separately</a> but can be connected to Maggot by specifying the corresponding URL in the <a href="#settings-incconfigconfiginc">configuration file</a>. Users and their rights are managed in the filebrowser application. Likewise, we can also <a href="../images/filebrowser_fig2.png" data-lightbox="fig2">create links to the data without a password</a>. These links can be usefully specified as external resources in the metadata managed by Maggot.</p>
 <p><center>
 <a href="../images/filebrowser_fig1.png" data-lightbox="fig10"><img src="../images/filebrowser_fig1.png" width="800px"></a><br>
  <em>See how to do install in <a href="https://github.com/djacob65/maggot-fb" target="_blank">github</a>.</em>
@@ -1232,7 +1232,7 @@ <h3 id="definitions-metadata-definition-files">Metadata definition files<a class
 <p>There are <strong>two levels of definition files</strong> as shown the figure below:</p>
 <p><center><a href="../images/definitions_fig2.png" data-lightbox="fig2"><img src="../images/definitions_fig2.png" width="600px"></a></center></p>
 <p><strong>1</strong> - The first level concerns the definition of terminology (metadata) similar to a <a href="https://sustainableheritagenetwork.org/system/files/atoms/file/How_to_Create_a_Descriptive_Metadata_Plan.pdf" target="_blank">descriptive metadata plan</a>. Clearly, this category is more akin to configuration files. They represent the heart of the application around which everything else is based. The input and search interfaces are completely generated from these definition files (especially the <em><a href="#definitions-terminology">web/conf/config_terms.txt</a></em> file), thus defining each of the fields, their <a href="../images/terminology_types.png" data-lightbox="fig3">input type</a> (<em>checkbox</em>, <em>dropbox</em>, <em>textbox</em>, ...) and the associated <a href="#definitions-vocabulary">controlled vocabulary</a> (ontology and thesaurus by <abbr title="feature in which an application predicts the rest of a word a user is typing">autocompletion</abbr>, drop-down list according to a list of fixed terms). This is why a <a href="#configuration">configuration step</a> is essential in order to be able to configure all the other modules.</p>
-<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="#definitions-dataverse">Dataverse</a>, <a href="#definitions-zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="#definitions-json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="#definitions-oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (<em><a href="https://github.com/inrae/pgd-mmdt/blob/main/web/inc/config/config.inc" target="_blank">web/inc/config/config.inc</a></em>).</p>
+<p><strong>2</strong> - The second level concerns the definitions of the mapping to a differently structured metadata schema (<a href="https://en.wikipedia.org/wiki/Schema_crosswalk" target="_blank">metadata crosswalk</a>, <em>i.e</em> a specification for mapping one metadata standard to another), used either <strong><em>i)</em></strong> for metadata export to a remote repository (<em>e.g.</em> <a href="#definitions-dataverse">Dataverse</a>, <a href="#definitions-zenodo">Zenodo</a>) or <strong><em>ii)</em></strong> for metadata harvesting (<em>e.g.</em> <a href="#definitions-json-ld"><abbr title="JavaScript Object Notation : format used to represent structured information">JSON</abbr>-LD</a>, <a href="#definitions-oai-pmh">OAI-PMH</a>). Simply place the definition files in the configuration directory (<em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>) for them to be taken into account, provided you have adjusted the configuration (See <a href="#settings-incconfigconfiginc">Settings</a>).</p>
 <p>All definition files are made using a simple spreadsheet then exported in <abbr title="Open text format representing tabular data as &quot;Tab-Separated Values&quot;. Each row corresponds to a table row and the cells in a row are separated by a tab">TSV</abbr> format. </p>
 <p>The list of definition files in Maggot are given below. All must be put under the directory <em><a href="https://github.com/inrae/pgd-mmdt/tree/main/web/conf" target="_blank">web/conf</a></em>.
 <center><a href="https://pmb-bordeaux.fr/maggot/config/view" target="_blank"><img src="../images/definitions_fig1.png" width="600px"></a></center></p>

tutorial/describe/index.html

@@ -844,7 +844,7 @@ <h1 id="quick-tutorial">Quick tutorial<a class="headerlink" href="#quick-tutoria
 
 <h3 id="metadata-entry">Metadata Entry<a class="headerlink" href="#metadata-entry" title="Permanent link">&para;</a></h3>
 <p>The figures are given here for illustration purposes but certain elements may be different for you given that this will depend on the configuration on your instance, in particular the choice of metadata, and the associated vocabulary sources.</p>
-<p>Indeed, the choice of vocabulary sources (ontologies, thesauri, dictionaries) as well as the choice of metadata fields to enter must in principle have been the subject of discussion between data producers and <abbr title="The data manager is the person who sets the data policy, i.e. its implementation and governance.">data manager</abbr> during the implementation of the Maggot tool in order to find the best compromise between the choice of sources and all the scientific fields targeted (see <a href="../../definitions">Definition files</a>). However a later addition is always possible.</p>
+<p>Indeed, the choice of vocabulary sources (ontologies, thesauri, dictionaries) as well as the choice of metadata fields to enter must in principle have been the subject of discussion between <abbr title="The data producers are the people who produced data and by extension have rights over it. They are also those who have the best knowledge of it.">data producers</abbr> and <abbr title="The data manager is the person who sets the data policy, i.e. its implementation and governance.">data manager</abbr> during the implementation of the Maggot tool in order to find the best compromise between the choice of sources and all the scientific fields targeted (see <a href="../../definitions">Definition files</a>). However a later addition is always possible.</p>
 <p><br></p>
 <h4 id="overview">Overview<a class="headerlink" href="#overview" title="Permanent link">&para;</a></h4>
 <p>When you enter the metadata entry module you should see a page that looks like the figure below:</p>