Ecoportal by MajidFiaz · Pull Request #91 · ontoportal/documentation

MajidFiaz · 2026-02-24T12:13:04Z

Hi, please review it.
Majid from LifeWatch ERIC

jonquet · 2026-02-24T13:19:45Z

@imadbourouche can you do this review and merge PR ?

jonquet · 2026-02-24T13:21:59Z

@MajidFiaz can you describe a bit the changes in the PR ... with no description at all it's way more work on the others side.

And is everything ok (running) on your side? I mean this is not software. Only website so we should be efficient with this.

MajidFiaz · 2026-02-24T13:44:39Z

Thank you for the comment.

This PR focuses specifically on updating the EcoPortal documentation, based on the latest official PDF version:

https://www.lifewatch.eu/wp-content/uploads/2025/06/SLW-00206-1-EcoPortal-Documentation.pdf

Summary of Changes

Updated EcoPortal documentation content to align with the PDF version linked above.

Adjusted structure and content to follow the current repository organization.

Modified shared sections where necessary to reflect EcoPortal-specific updates.

Since some content is shared across other portal documentations (EarthPortal, OntoPortal), there may be structural or shared-content impacts. However, I followed the existing structure in the repository to keep consistency and avoid unnecessary changes outside EcoPortal.

Preview / Verification

You can review the rendered version here:

https://majidfiaz.github.io/documentation/

Everything is building and rendering correctly on my side.

jonquet · 2026-03-10T09:24:42Z

@imadbourouche Can you review and merge the PR ?
@alexskr Can you confirm this is ok with your recent changes ?

imadbourouche · 2026-03-12T16:02:36Z

_includes/shared_doc/ontology_lifecycle/feedback.md

-{{ page.portal }} includes some community-oriented features such as: (ii) notes that can be attached in a forum-like mode to a specific artefact or class/concept, in order to discuss the ontology (its design, use, or evolution) or allow users to propose changes. (iii) change requests can be submitted, and in some cases directly transferred to external systems such as a GitHub issue tracker.
-Administrators encourage the users to engage in giving feedback on {{ page.atoms }} since each input is valuable in developing and publishing community-approved artefacts.
+## Give feedback on semantic artefacts
+{{ page.portal }} includes some community-oriented features in the [notes]({{ site.baseurl }}{% link docs/users-guide-docs/documentation/ecoportal/platform_overview/ontology_details.md %}) such as: (i) comments that can be attached in a forum-like mode to a specific artefact or class/concept, in order to discuss different specifications of the semantic artefact (its design, use, or evolution) or allow users to propose changes, and (ii) proposals that can be submitted within the portal.


the link of the notes here is giving me 404 page not found locally

imadbourouche · 2026-03-12T16:04:38Z

_includes/shared_doc/ontology_lifecycle/feedback.md

-### Give feedback on {{ page.atoms }}
-{{ page.portal }} includes some community-oriented features such as: (ii) notes that can be attached in a forum-like mode to a specific artefact or class/concept, in order to discuss the ontology (its design, use, or evolution) or allow users to propose changes. (iii) change requests can be submitted, and in some cases directly transferred to external systems such as a GitHub issue tracker.
-Administrators encourage the users to engage in giving feedback on {{ page.atoms }} since each input is valuable in developing and publishing community-approved artefacts.
+## Give feedback on semantic artefacts


I think here we should let the {{ page.atoms }} so that each portal can specify if it uses the semantic artefacts or use another word like ontologies ..etc

imadbourouche · 2026-03-12T16:38:02Z

_includes/shared_doc/ontology_lifecycle/skos_support_3.md

+### Hierarchy in SKOS vocabularies

-The only semantic relationship in SKOS vocabularies that {{page.portal}} uses to construct and display concept hierarchies is the skos:broader property.
+The only semantic relationship in SKOS vocabularies that EcoPortal uses to construct and display concept hierarchies is the skos:broader property.


here we have to let the {{page.portal}} and not hard code the EcoPortal

imadbourouche · 2026-03-12T16:40:48Z

_includes/shared_doc/ontology_lifecycle/skos_support_4.md

-When examining metric tables within the {{ page.portal }} user interface, the "Number Of Individuals" value aligns with the count of concepts within a given SKOS vocabulary.
+### Metrics data for SKOS vocabularies
+
+{{ page.portal }} employs the [OWL API](https://owlcs.github.io/owlapi/) to parse all ontology and vocabulary submissions, including the computation of metric data. The OWL API interprets SKOS vocabularies as RDF files that encompass classes and instances. Following the SKOS Reference, concepts are identified as instances of owl:Class, consequently, they are counted as instances, also referred to as "individuals".


the local links in this section are showing 404 page not found

imadbourouche · 2026-03-12T16:42:54Z

_includes/shared_doc/ontology_lifecycle/skos_support_5.md

 This example provides a simple illustration of the composition of a SKOS file that complies with the above constraints.
- **Example header**. The provided header establishes several common namespaces that could prove valuable. The final namespace is the one responsible for defining the specific SKOS vocabulary in question. Ideally, the IRI associated with the "myskosid" namespace should be a resolvable location pointing to the SKOS ontology.
-    ```
+- **Example header**. The provided header establishes several common namespaces that could prove valuable. The final namespace is the one responsible for defining the specific SKOS vocabulary in question. Ideally, the IRI associated with the "myskosid" namespace should be a resolvable location pointing to the SKOS semantic artefact.


here use {{page.atom}}

imadbourouche · 2026-03-12T16:56:38Z

_includes/shared_doc/ontology_lifecycle/update_2.md

+**Edit submission**

-From this section, located at the top right corner, the {{ page.atom }} administrators can change the settings of a {{ page.atom }} (e.g., name, administrators, viewing restrictions, categories, etc.). It is not possible to change the {{ page.atom }} acronym because {{ page.portal }} uses this field as a primary key and identifier. 
+The editing of semantic artefacts metadata can be performed in two ways: edits of a specific version of the resource (“Pencil” button on the bottom left corner, Figure 45.2), edits of the latest submission (“Pencil” button on the top right corner, Figure 45.1). __It is not possible to change the semantic artefact acronym because EcoPortal uses this field as a primary key and identifier__. Once the form is edited, click on the "Save" button. If the "Location" settings are not changed,  only the metadata changes will be saved.


use {{page.atom}} and don't hardcode EcoPortal because it's shared doc

imadbourouche · 2026-03-12T16:57:06Z

_includes/shared_doc/ontology_lifecycle/update_3.md

-From this section, located at the bottom left corner, the {{ page.atom }} manager(s) can upload a new version of the existing {{ page.atom }} and update the metadata using one of the following two options:
- If in the original submission was set up an automatic update of the resource from a source URL, {{ page.portal }} examines the content of this URL nightly, and re-submits the content if it has changed . If the updated submission does not parse, the {{ page.atom }} manager(s) will be notified via email;
- If in the original submission was not set up an automatic update of the resource, or if the {{ page.atom }} manager(s) want to immediately update the {{ page.atom }}, they can upload the new version directly by selecting a local file. The upload process starts and the {{ page.atom }} will be parsed shortly thereafter. {{ page.atom }} manager(s) can at this point also change the settings and enable the automatic update of the resource. The {{ page.atom }} parsing is completed within an hour maximum with the exception of large {{ page.atoms }}, whereas {{ page.atom }} indexing and automatic mapping occur overnight (Pacific Time).
+From this section, located at the top right corner (see Figure 45.1), the semantic artefact manager(s) can upload a new version of the existing semantic artefact and update the metadata using one of the following two options:


let {{page.atom}}

imadbourouche · 2026-03-12T16:57:47Z

_includes/shared_doc/ontology_lifecycle/update_3.md

+- If in the original submission was set up an automatic update of the resource from a source URL, {{ page.portal }} examines the content of this URL nightly, and re-submits the content if it has changed. If the updated submission does not parse, the semantic artefact manager(s) will be notified via email;
+- If in the original submission was not set up an automatic update of the resource, or if the semantic artefact manager(s) want to immediately update the semantic artefact, they can upload the new version directly by selecting a local file. The upload process starts and the semantic artefact will be parsed shortly thereafter. Semantic artefact manager(s) can at this point also change the settings and enable the automatic update of the resource. The semantic artefact parsing is completed within an hour maximum with the exception of large semantic artefacts, whereas semantic artefact indexing and automatic mapping occur overnight.
+
+![1. Editing section 2. Submission section]({{site.figures_link}}/{{page.portal}}/Figure45.png)


the figure45 is not showing in this page

imadbourouche · 2026-03-12T17:04:36Z

_includes/shared_doc/platform_overview/ontology_details/summary/index.md

@@ -1,3 +1,9 @@
-## Summary
+On the left side of the summary page, below the general information box, there are two buttons for downloading metadata of different formats:


the name of the file index.md is not aligned with the section content metadata buttons.

imadbourouche · 2026-03-12T17:05:50Z

_includes/shared_doc/platform_overview/ontology_details/summary/summary_metadata_metrics_1.md

@@ -1,2 +1,75 @@
 ### Metrics
-This section describes the metrics that {{ page.portal }} computes for each semantic artefact (Figure 7). Metrics start to be computed when a semantic artefact is uploaded and they are part of {{ page.portal }} Metadata Schema.
+This section describes the metrics that {{ page.portal }} computes for each semantic artefact (Figure 15). Metrics start to be computed when a semantic artefact is uploaded and they are part of the [EcoPortal Metadata Schema]({{ site.baseurl }}{% link docs/users-guide-docs/documentation/ecoportal/metadata_schema.md %}). By clicking on the window icon next to “Classes”, “Individuals” and “Properties”, users can access the graph showing the evolution of the number of classes/individuals/properties of the selected semantic artefact.


this is shared section, use special section/file for the ecoportal content here

Majid added 30 commits January 27, 2025 12:40

first commit

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update homepage

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update homepage in sub manu

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update homepage in sub manu

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testing

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updated navigation

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completed homepage

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working on tool

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working on tool

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working on tool

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completed tool

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completed till Classes/Concepts

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semantic completed

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table testing

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table added

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table fixed issues

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create and edit semantic

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added images for create and edit semantic

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deleted extra

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sementic completed

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fixed issues: 12-13-17-18

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fixed issued 19

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fixed issued 26

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fixed issued 25

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fixed issued 24-23

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fixed issued 21

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fixed issued 22

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checking navigation

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checking navigation

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checking navigation1

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Majid added 20 commits February 25, 2025 11:31

testing

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testing

b752cee

testing

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testing

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updated links

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updated links

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updated almost all links

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updated bold and italic

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updated api documentation

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updated api key image

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updated api documentation

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fixed issue 34 and others

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fixed issues

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updated ecoportal widget

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figure 46 fixed

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updated text

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deleted rest api documentation

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added api key title

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change links to api documentation

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merging other repo

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jonquet requested review from alexskr and imadbourouche March 10, 2026 09:23

jonquet added the documentation Improvements or additions to documentation label Mar 10, 2026

jonquet assigned alexskr Mar 10, 2026

jonquet removed the request for review from alexskr March 10, 2026 09:25

imadbourouche suggested changes Mar 12, 2026

View reviewed changes

		@@ -1,3 +1,9 @@
		## Summary
		On the left side of the summary page, below the general information box, there are two buttons for downloading metadata of different formats:

Conversation

MajidFiaz commented Feb 24, 2026

Uh oh!

jonquet commented Feb 24, 2026

Uh oh!

jonquet commented Feb 24, 2026

Uh oh!

MajidFiaz commented Feb 24, 2026

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jonquet commented Mar 10, 2026

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