Merge pull request #59 from galviset/feature/federated-content-ecopor…

…tal (Portal documentation: EcoPortal)

Portal documentation: EcoPortal

docs/users-guide-docs/documentation/ecoportal/about.md

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+---
+layout: default
+title: About
+permalink: user_guide/EcoPortal
+parent: Users guide
+nav_order: 1
+portal: "EcoPortal"
+atom: "semantic artefact"
+atoms: "semantic artefacts"
+---
+{% include documentation_nav.html portal="EcoPortal" portal="EcoPortal"  %}
+
+# About EcoPortal
+
+### What is EcoPortal and who developed it?
+EcoPortal is a repository of semantic artefacts in the ecological domain. EcoPortal was developed by [LifeWatch ERIC](https://www.lifewatch.eu/), in collaboration with its Italian node [LifeWatch Italy](https://www.lifewatchitaly.eu/) coordinated by [CNR](https://www.cnr.it/), through the reuse of the OntoPortal technology to support the activities of different kinds of stakeholders (researchers, vocabularies managers, data managers, ontologists, etc.). EcoPortal assists the community in the creation, management, mapping and alignment of FAIR semantic artefacts, which make the meaning of research data clear and explicit, ultimately increasing their impact. 
+
+### Why EcoPortal and how it works?
+In the last decade, ecological research groups and research infrastructures have contributed to the production of numerous vocabularies and ontologies to increase data discovery, integration and interoperability. To make the discovery and use of all these semantic artefacts easier, [LifeWatch ERIC](https://www.lifewatch.eu/) developed EcoPortal. The platform acts as an access point for semantic artefacts, allowing users to maximise the efficiency of search, annotation and other scientific data management processes as well as to perform specific tasks. All of these functions are seamlessly integrated within a fully compliant semantic web infrastructure.

docs/users-guide-docs/documentation/ecoportal/developer_guide/api_key.md

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+---
+title: API Key @EcoPortal
+summary: How to fetch your API key and use it
+layout: default
+parent: Developer guide @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/api_key/EcoPortal
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% include shared_doc/developer_guide/api_key.md  %}
+{% include shared_doc/developer_guide/api_key_examples.md  %}

docs/users-guide-docs/documentation/ecoportal/developer_guide/index.md

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+---
+title: Developer guide @EcoPortal
+summary: Show relevant features for developers who wants to use EcoPortal in their projects
+layout: default
+parent: Users guide
+permalink: user_guide/developer_guide/EcoPortal
+has_children: true
+nav_order: 5
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+## Developer guide
+{% include shared_doc/developer_guide/index.md  %}

docs/users-guide-docs/documentation/ecoportal/developer_guide/use_cases.md

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+---
+title: Use cases @EcoPortal
+summary: Few examples on what to use EcoPortal for
+layout: default
+parent: Developer guide @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/use_cases/EcoPortal
+nav_order: 2
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% include shared_doc/developer_guide/usecases.md  %}

docs/users-guide-docs/documentation/ecoportal/developer_guide/widgets.md

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+---
+title: Widgets @EcoPortal
+summary: How to implement EcoPortal widgets in your projects
+layout: default
+parent: Developer guide @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/developer_guide/widgets/EcoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% 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  %}

docs/users-guide-docs/documentation/ecoportal/metadata_schema.md

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+---
+title: Metadata Schema
+summary: Description of the metadata schema
+layout: default
+parent: Users guide
+permalink: user_guide/metadata_schema/EcoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+{% include shared_doc/metadata_schema/MOD.md  %}

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/feedback.md

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+---
+title: Give feedback
+summary: How to to give feedback on semantic artefacts
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/feedback/EcoPortal
+nav_order: 5
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/feedback.md  %}

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/index.md

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+---
+title: Semantic artefacts lifecycle @EcoPortal
+summary: Describes how to manage semantic artefacts on the portal
+layout: default
+parent: Users guide
+permalink: user_guide/ontology_lifecycle/EcoPortal
+has_children: true
+nav_order: 4
+---
+
+{% include documentation_nav.html %}
+
+This section contains guidelines for managing {{page.atoms}}.

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/skos_support.md

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+---
+title: SKOS Support
+summary: How is SKOS supported in EcoPortal
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/skos_support/EcoPortal
+nav_order: 6
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% 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  %}

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/submit.md

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+---
+title: Submit new semantic artefacts
+summary: How to submit a new semantic artefact
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/submit/EcoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% include shared_doc/ontology_lifecycle/submit_1.md  %}
+{% include shared_doc/ontology_lifecycle/submit_2.md  %}

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/update.md

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+---
+title: Update
+summary: How to update a submitted semantic artefact
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/update/EcoPortal
+nav_order: 4
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% 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  %}

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/vocbench_create.md

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+---
+title: Create and edit
+summary: How to export semantic artefacts from VocBench
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/vocbench_create/EcoPortal
+nav_order: 1
+---
+
+[VocBench EcoPortal](https://vocbench.lifewatchitaly.eu/vocbench3/) is a service that enables the creation, editing and publishing of semantic artefacts in the ecological domain. 
+To create a new project or edit an existing project in **VocBench EcoPortal** there are two options:
+1. **Not registered users** must register to VocBench EcoPortal at the following [link](https://vocbench.lifewatchitaly.eu/vocbench3/). 
+Within the registration form, it is possible to request editing permission of a semantic artefact published in EcoPortal by adding the full resource name and acronym (e.g., [Fish Traits Thesaurus (FISHTRAITS)](http://ecoportal.lifewatchitaly.eu/ontologies/FISHTRAITS)) into the box “Existing semantic artefact?”. By default, the last version on EcoPortal is loaded, otherwise users have to specify the version from which to start editing in VocBench. NOTE: Only the semantic artefact owner can request editing permission of that resource. 
+To create a new semantic artefact users must specify:
+    - *New semantic artefact*: the name of the project, e.g., Fish Traits Thesaurus. It is recommended to add the full name of the resource that will appear in EcoPortal;
+    - *BaseURI*: the URL necessary for the creation of a project. **NOTE**: if users do not have a BaseURI, the system will provide the following: 
+        - https://kos.lifewatch.eu/ontologies/yourACRONYM for ontologies;
+        - https://kos.lifewatch.eu/thesauri/yourACRONYM for thesauri, glossaries or other loose sets of concepts.
+    - *Model*: the model of the new project which can be [OWL](https://www.w3.org/TR/owl-features/) or [SKOS](https://www.w3.org/TR/skos-reference/). **NOTE**: To understand more about the SKOS model in EcoPortal it is recommended to read the following section. 
+
+![Registration in VocBench and creation of a new semantic artefact]({{site.figures_link}}/{{include.portal}}/vocbench_registration.png)
+
+2. **Registered users** can contact the Administrators at this email address semantics@lifewatch.eu, specifying: 
+   1. name of the new semantic artefact
+   2. Base URI (check the previous paragraph for more specific information)
+   3. Model (e.g. OWL, SKOS, RDFS, OntoLex, EDOAL)
+   4. Lexicalization (e.g. RDFS, SKOS, SKOS-XL, OntoLex)
+   5. specify which among history, validation, blacklisting, undo, trivial inference to have
+   6. repository access (e.g. create a local project or a remote one), 7. configuration (e.g. native store, in memory, GraphDB)
+The request is then managed by the administrator that will create the new project and assign the role of [Project Manager](http://vocbench.uniroma2.it/doc/user/roles_adm.jsf) to the creator. 
+
+In the list of projects, there should be a new item for the project as shown below, with information related to name, model and lexicalization of the resource. It is indicated whether history and validation have been activated  in the project. Lastly, the repository location is specified (e.g. local or remote).
+
+![List of projects in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_projects.png)
+All subsequent steps require moving to the “Data” tab to edit the semantic artefact. In the “Scheme” tab, click on the create button to create a new skos:ConceptScheme ( []* ).
+
+![Scheme tab of the project in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_schemes.png)
+In the scheme creation dialog, specify the label of the concept scheme e.g., “continents” in English and then click on the **Ok** button.
+
+![Creation of a concept scheme in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_schemes_create.png)
+Then, select the newly created scheme as shown below.
+
+![Selection of a newly created scheme in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_schemes_created.png)
+In the Concept tab, click on the create button to create a new skos:Concept ( ()* ).
+
+![Concept tab of the project in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_concepts.png)
+In the concept creation dialog, specify the label of the concept e.g., “Africa” in English and then click on the Ok button. This label represents the skos:prefLabel of the concept.
+
+![Creation of a new concept in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_concepts_new.png)
+Do the same to create other concepts:
+- America
+- Asia
+- Europe
+- Oceania
+- Antarctica
+The concept tree generated should contain a flat list of the five continents (Figure 29). It should be noted that the list of concepts generated is visualised in alphabetical order.
+
+![The concept tree in VocBench]({{site.figures_link}}/{{include.portal}}/vocbench_concepts_tree.png)
+To add hierarchical depth to the structure, in the concept tab (Figure 30) select one continent and click on “Create narrow concept” button ( ()* ).
+![Create narrow concept]({{site.figures_link}}/{{include.portal}}/vocbench_concepts_create_narrow.png)
+In the creation dialog (Figure 31), specify the label for the narrow concept e.g., “Italy” in English and then click on the Ok button.
+![Wizard for the creation of narrower concept]({{site.figures_link}}/{{include.portal}}/vocbench_create_wizard.png)
+To understand in detail the different aspects of the user experience on VocBench, we recommend reading the following [User Manual](https://vocbench.uniroma2.it/doc/user/).
+
+### Import an excel into VocBench
+VocBench uses the platform **Sheet2RDF** to generate RDF triples from datasheets. Sheet2RDF can be accessed by clicking on the Tool tab of the VocBench menu and selecting the Sheet2RDF entry. 
+To use the Sheet2RDF tool correctly, it is essential to compile with the correct formatting where by each datasheet column represents a SKOS/OWL property. An illustrative example of a valid file format is provided [here](https://docs.google.com/spreadsheets/d/1PHw0AaiEdk9EoKBBBCNeLCczuHxbHf5B/edit?usp=sharing&ouid=112643334527918409138&rtpof=true&sd=true). For a comprehensive understanding of the user interface and the diverse functionalities of the tool, please consult this [resource](https://art.uniroma2.it/sheet2rdf/documentation/vb_tool/). The following example provides details about the SKOS concepts creation when using Sheet2RDF.
+
+**Example**:
+After uploading the Excel file using the "Browse" button, select "Subject mapping" in red (see Figure 32). Users are then required to:
+1. Select the header that is going to be your Subject;
+2. Select on the “Assert type” check box;
+3. Click on the yellow circle and select “Concept”;
+4. In the “Converter” tab below, select “DefaultConverter”;
+5. In “Additional predicate-object” tab, click on the “plus” button on the side;
+6. Add the Predicate by selecting the SKOS property “inScheme”;
+7. Then select the Object by clicking on “Concept Scheme” and then on the scheme that you desire;
+8. Then click “OK”.
+**Note**: the Concept Scheme has to be created before uploading the SKOS concepts.
+
+![Subject header editor]({{site.figures_link}}/{{include.portal}}/vocbench_subject_editor.png)
+Upon executing these tasks, all headers should be highlighted in **green** (Figure 33).
+
+![Sheet2RDF tool]({{site.figures_link}}/{{include.portal}}/vocbench_sheet2RDF.png)
+If a header appears in **yellow** or **black**, clicking on the pencil icon next to the header will give the possibility to either manually map the SKOS/OWL property or ignore the header. Following this, the blue "play" button and the subsequent green one should be clicked to generate the PURL code and triples. After the triples are generated, navigating to the "Generated triples preview" tab allows users to click on the "Add triples" button, presenting all the information in the "Data" section.

docs/users-guide-docs/documentation/ecoportal/ontology_lifecycle/vocbench_export.md

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+---
+title: Export from VocBench
+summary: How to create and edit semantic artefacts
+layout: default
+parent: Semantic artefacts lifecycle @EcoPortal
+grand_parent: Users guide
+permalink: user_guide/ontology_lifecycle/vocbench_export/EcoPortal
+nav_order: 2
+---
+
+## Export a semantic artefact from VocBench
+To export to EcoPortal the semantic artefacts created, users have to access the “Global Data Management” menu and click on “Export data”. Users then have to choose the export format and click on the “submit” button.
+
+![Global Data Management export]({{site.figures_link}}/{{include.portal}}/vocbench_gdm_export.png)

docs/users-guide-docs/documentation/ecoportal/platform_overview/homepage.md

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+---
+title: Homepage
+summary: EcoPortal homepage
+layout: default
+parent:  EcoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/homepage/EcoPortal
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% 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  %}
+

docs/users-guide-docs/documentation/ecoportal/platform_overview/index.md

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+---
+title: EcoPortal overview
+summary: Overview page
+layout: default
+parent: Users guide
+permalink: user_guide/platform_overview/EcoPortal
+has_children: true
+nav_order: 1
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}

docs/users-guide-docs/documentation/ecoportal/platform_overview/ontology_details.md

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+---
+title: Details page
+summary: Details page of semantic artefacts
+layout: default
+parent:  EcoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/ontology_details/EcoPortal
+nav_order: 3
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+## 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  %}

docs/users-guide-docs/documentation/ecoportal/platform_overview/tools.md

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+---
+title: Tools
+summary: EcoPortal tools
+layout: default
+parent:  EcoPortal overview
+grand_parent: Users guide
+permalink: user_guide/platform_overview/tools/EcoPortal
+nav_order: 2
+---
+
+{% include documentation_nav.html portal="EcoPortal"  %}
+
+{% 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  %}
+
+### Mappings
+{% include shared_doc/platform_overview/tools/mapping/mappings.md  %}
+{% include shared_doc/platform_overview/tools/mapping/sources.md  %}
+
+### Recommender
+{% include shared_doc/platform_overview/tools/recommender/recommender.md  %}
+
+{% include shared_doc/platform_overview/tools/vocbench/vocbench.md  %}