Merge pull request #61 from galviset/feature/federated-content-ontopo…

…rtal (Portal documentation: default OntoPortal) Portal documentation: default OntoPortal
ontoportal · Jul 4, 2024 · 083c66d · 083c66d
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diff --git a/docs/users-guide-docs/documentation/ontoportal/about.md b/docs/users-guide-docs/documentation/ontoportal/about.md
@@ -4,5 +4,8 @@ title: About
 permalink: user_guide/OntoPortal
 parent: Users guide
 nav_order: 1
+portal: "OntoPortal"
+atom: "ontology"
+atoms: "ontologies"
 ---
 {% include documentation_nav.html portal="OntoPortal" %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/developer_guide/api_key.md b/docs/users-guide-docs/documentation/ontoportal/developer_guide/api_key.md
@@ -0,0 +1,14 @@
+---
+title: API Key
+summary: How to fetch your API key and use it
+layout: default
+parent: Developer guide @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/api_key/OntoPortal
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/developer_guide/api_key.md  %}
+{% include shared_doc/developer_guide/api_key_examples.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/developer_guide/index.md b/docs/users-guide-docs/documentation/ontoportal/developer_guide/index.md
@@ -0,0 +1,14 @@
+---
+title: Developer guide @OntoPortal
+summary: Show relevant features for developers who wants to use OntoPortal in their projects
+layout: default
+parent: Users guide
+permalink: user_guide/developer_guide/OntoPortal
+has_children: true
+nav_order: 5
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+## Developer guide
+{% include shared_doc/developer_guide/index.md %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/developer_guide/use_cases.md b/docs/users-guide-docs/documentation/ontoportal/developer_guide/use_cases.md
@@ -0,0 +1,13 @@
+---
+title: Use cases
+summary: Few examples on what to use OntoPortal for
+layout: default
+parent: Developer guide @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/use_cases_OntoPortal/OntoPortal
+nav_order: 2
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/developer_guide/usecases.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/developer_guide/widgets.md b/docs/users-guide-docs/documentation/ontoportal/developer_guide/widgets.md
@@ -0,0 +1,17 @@
+---
+title: Widgets
+summary: How to implement OntoPortal widgets in your projects
+layout: default
+parent: Developer guide @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/widgets/OntoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/developer_guide/widgets_intro.md  %}
+{% include shared_doc/developer_guide/widgets_search.md  %}
+{% include shared_doc/developer_guide/widgets_term_selection.md  %}
+{% include shared_doc/developer_guide/widgets_tree.md  %}
+{% include shared_doc/developer_guide/widgets_visualization.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/metadata_schema.md b/docs/users-guide-docs/documentation/ontoportal/metadata_schema.md
@@ -0,0 +1,11 @@
+---
+title: Metadata Schema
+summary: Description of the metadata schema
+layout: default
+parent: Users guide
+permalink: user_guide/metadata_schema/OntoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+{% include shared_doc/metadata_schema/BioPortal.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/feedback.md b/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/feedback.md
@@ -0,0 +1,13 @@
+---
+title: Give feedback
+summary: How to to give feedback on ontologies
+layout: default
+parent: Semantic artefacts lifecycle @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/feedback/OntoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/feedback.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/index.md b/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/index.md
@@ -0,0 +1,13 @@
+---
+title: Semantic artefacts lifecycle @OntoPortal
+summary: Describes how to manage ontologies on the portal
+layout: default
+parent: Users guide
+permalink: user_guide/ontology_lifecycle/OntoPortal
+has_children: true
+nav_order: 4
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+This section contains guidelines for managing {{page.atoms}}.
diff --git a/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/skos_support.md b/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/skos_support.md
@@ -0,0 +1,17 @@
+---
+title: SKOS Support
+summary: How is SKOS supported in OntoPortal
+layout: default
+parent: Semantic artefacts lifecycle @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/skos_support/OntoPortal
+nav_order: 4
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/skos_support_1.md  %}
+{% include shared_doc/ontology_lifecycle/skos_support_2.md  %}
+{% include shared_doc/ontology_lifecycle/skos_support_3.md  %}
+{% include shared_doc/ontology_lifecycle/skos_support_4.md  %}
+{% include shared_doc/ontology_lifecycle/skos_support_5.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/submit.md b/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/submit.md
@@ -0,0 +1,14 @@
+---
+title: Submit new ontologies
+summary: How to submit a new ontology
+layout: default
+parent: Semantic artefacts lifecycle @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/submit/OntoPortal
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/submit_1.md  %}
+{% include shared_doc/ontology_lifecycle/submit_2.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/update.md b/docs/users-guide-docs/documentation/ontoportal/ontology_lifecycle/update.md
@@ -0,0 +1,16 @@
+---
+title: Update
+summary: How to update a submitted ontology
+layout: default
+parent: Semantic artefacts lifecycle @OntoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/update/OntoPortal
+nav_order: 2
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/update_1.md  %}
+{% include shared_doc/ontology_lifecycle/update_2.md  %}
+{% include shared_doc/ontology_lifecycle/update_3.md  %}
+{% include shared_doc/ontology_lifecycle/update_4.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/platform_overview/homepage.md b/docs/users-guide-docs/documentation/ontoportal/platform_overview/homepage.md
@@ -0,0 +1,23 @@
+---
+title: Homepage
+summary: OntoPortal homepage
+layout: default
+parent:  OntoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/homepage/OntoPortal
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/platform_overview/homepage/index.md  %}
+
+### Search and Metrics
+{% include shared_doc/platform_overview/homepage/search_and_metrics.md  %}
+
+### O'FAIRe tool
+{% include shared_doc/platform_overview/homepage/ofaire.md  %}
+
+### Account settings
+{% include shared_doc/platform_overview/homepage/account_settings.md  %}
+
diff --git a/docs/users-guide-docs/documentation/ontoportal/platform_overview/index.md b/docs/users-guide-docs/documentation/ontoportal/platform_overview/index.md
@@ -0,0 +1,11 @@
+---
+title: OntoPortal overview
+summary: Overview page
+layout: default
+parent: Users guide
+permalink: user_guide/platform_overview/OntoPortal
+has_children: true
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
diff --git a/...users-guide-docs/documentation/ontoportal/platform_overview/ontology_details.md b/...users-guide-docs/documentation/ontoportal/platform_overview/ontology_details.md
@@ -0,0 +1,42 @@
+---
+title: Details page
+summary: Details page of ontologies
+layout: default
+parent:  OntoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/ontology_details/OntoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+## Semantic Artefact details
+{% include shared_doc/platform_overview/ontology_details/sa_details_main.md  %}
+{% include shared_doc/platform_overview/ontology_details/sa_details_screenshot.md  %}
+{% include shared_doc/platform_overview/ontology_details/sa_details_side.md  %}
+
+## Metadata Summary
+{% include shared_doc/platform_overview/ontology_details/summary/index.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_schema.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_export.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_fair.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_1.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_2.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_3.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_4.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_5.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_6.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_submissions.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_views.md  %}
+{% include shared_doc/platform_overview/ontology_details/summary/summary_metadata_projects.md  %}
+
+
+## Menu
+{% include shared_doc/platform_overview/ontology_details/menu/index.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_classes.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_properties.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_notes.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_mappings.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_schemes.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_collections.md  %}
+{% include shared_doc/platform_overview/ontology_details/menu/menu_widgets.md  %}
diff --git a/docs/users-guide-docs/documentation/ontoportal/platform_overview/tools.md b/docs/users-guide-docs/documentation/ontoportal/platform_overview/tools.md
@@ -0,0 +1,29 @@
+---
+title: Tools
+summary: OntoPortal tools
+layout: default
+parent:  OntoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/tools/OntoPortal
+nav_order: 2
+---
+
+{% include documentation_nav.html portal="OntoPortal"  %}
+
+{% include shared_doc/platform_overview/tools/tools.md  %}
+
+### Browse
+{% include shared_doc/platform_overview/tools/browse/browse.md  %}
+{% include shared_doc/platform_overview/tools/browse/filters.md  %}
+{% include shared_doc/platform_overview/tools/browse/submit.md  %}
+
+### Search
+{% include shared_doc/platform_overview/tools/search/search.md  %}
+
+### Annotator
+{% include shared_doc/platform_overview/tools/annotator/annotator.md  %}
+
+### Recommender
+
+### Mappings
+