Merge pull request #748 from dgarijo/develop

Adding CodeMeta file
dgarijo · Feb 13, 2025 · 5d9b0e7 · 5d9b0e7
2 parents f354014 + 93c92f6
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -54,11 +54,11 @@ jobs:
       # https://github.com/docker/metadata-action (lower cases image name, etc.)
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@v5.5.1
+        uses: docker/metadata-action@v5.6.1
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
       - name: Build and push
-        uses: docker/build-push-action@v6.6.1
+        uses: docker/build-push-action@v6.13.0
         with:
           push: ${{ github.event_name != 'pull_request' && github.actor != 'dependabot[bot]' }}
           tags: ${{ steps.meta.outputs.tags }}

diff --git a/codemeta.json b/codemeta.json
@@ -0,0 +1,62 @@
+{
+    "@context": "https://w3id.org/codemeta/3.0",
+    "@type": "SoftwareSourceCode",
+    "license": {
+      "name": "Apache License 2.0",
+      "url": "https://raw.githubusercontent.com/dgarijo/Widoco/master/LICENSE",
+      "identifier": "https://spdx.org/licenses/Apache-2.0"
+    },
+    "codeRepository": "https://github.com/dgarijo/Widoco",
+    "issueTracker": "https://github.com/dgarijo/Widoco/issues",
+    "dateCreated": "2013-07-15",
+    "dateModified": "2025-01-31",
+    "downloadUrl": "https://github.com/dgarijo/Widoco/releases",
+    "name": "Widoco",
+    "logo": "https://raw.githubusercontent.com/dgarijo/Widoco/master/src/main/resources/logo/logo2.png",
+    "keywords": "documentation, metadata, ontology, ontology-diagram, ontology-evaluation, wizard",
+    "programmingLanguage": [
+      "JavaScript",
+      "Java",
+      "XSLT",
+      "CSS",
+      "HTML",
+      "Dockerfile"
+    ],
+    "softwareRequirements": [
+      "Just add the dependency and repository to your `pom.xml` file as follows. See the [WIDOCO JitPack](https://jitpack.io/#dgarijo/Widoco) page to find alternative means to incorporate WIDOCO to your project.\n\n```xml\n<dependencies>\n  <dependency>\n      <groupId>com.github.dgarijo</groupId>\n      <artifactId>Widoco</artifactId>\n      <version>v1.4.24</version>\n  </dependency>\n</dependencies>\n\n[ ... ]\n\n<repositories>\n\t<repository>\n\t    <id>jitpack.io</id>\n\t    <url>https://jitpack.io</url>\n\t</repository>\n</repositories>\n```\n",
+      "You will need Java 1.8 or higher (SDK 1.8 or JRE 8) for WIDOCO to work\nOtherwise, you will probably experience an \"Unsupported major.minor version 52.0\" exception when executing the JAR file.\n"
+    ],
+    "releaseNotes": "This version of WIDOCO fixes documentation broken links, clarifies how to download Docker images and includes a new option for excluding the provenance page from documentation (thanks to @MikiDi) \r\n\r\n## What's Changed\r\n* Bump docker/build-push-action from 5.3.0 to 5.4.0 by @dependabot in https://github.com/dgarijo/Widoco/pull/709\r\n* CLI option to exclude provenance link by @MikiDi in https://github.com/dgarijo/Widoco/pull/710\r\n* Improved documentation (broken links)\r\n\r\n\r\n**Full Changelog**: https://github.com/dgarijo/Widoco/compare/v1.4.24...v1.4.25",
+    "softwareVersion": "v1.4.25",
+    "buildInstructions": [
+      "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md"
+    ],
+    "author": [
+      {
+        "@type": "Person",
+        "@id": "http://orcid.org/0000-0003-0454-7145"
+      }
+    ],
+    "referencePublication": [
+      {
+        "@type": "ScholarlyArticle",
+        "identifier": "10.1007/978-3-319-68204-4_9",
+        "author": {
+            "@type": "Person",
+            "givenName": "Daniel",
+            "familyName": "Garijo",
+            "@id": "http://orcid.org/0000-0003-0454-7145"
+          },
+        "url": "http://dgarijo.com/papers/widoco-iswc2017.pdf",
+        "name": "WIDOCO: a wizard for documenting ontologies",
+        "datePublished": "2017",
+        "pagination": "94--102"
+      }
+    ],
+    "identifier": "https://doi.org/10.5281/zenodo.11093793",
+    "readme": "https://raw.githubusercontent.com/dgarijo/Widoco/master/README.md",
+    "description": [
+      "Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template.",
+      "WIDOCO helps you to publish and create an enriched and customized documentation of your ontology, by following a series of steps in a wizard. We extend the LODE framework by Silvio Peroni to describe the classes, properties and data properties of the ontology, the OOPS! webservice by María Poveda to print an evaluation and the Licensius service by Victor Rodriguez Doncel to determine the license URI and title being used. In addition, we use WebVowl to visualize the ontology and have extended Bubastis to show a complete changelog between different versions of your ontology.\n\nFeatures of WIDOCO:\n* Automatic documentation of the terms in your ontology (based on [LODE](http://www.essepuntato.it/lode/)). Now **you can use Markdown on your class descriptions** (see [example](https://dgarijo.github.io/Widoco/doc/gallery/index.html))\n* Massive metadata extraction and support: WIDOCO will enhance your ontology documentation  based on your ontology annotations. Now you can add custom logos and images, edit the content of your sections, etc. by just editing metadata. See our [supported metadata](doc/metadataGuide/guide.md) and [recommendations](https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html) for more information.\n* Automatic annotation in JSON-LD snippets of the html produced.\n* Association of a provenance page which includes the history of your vocabulary (W3C PROV-O compliant).\n* Guidelines on the main sections that your document should have and how to complete them.\n* Integration with diagram creators ([WebVOWL](http://vowl.visualdataweb.org/webvowl/)).\n* Automatic changelog of differences between the actual and the previous version of the ontology (based on [Bubastis](http://www.ebi.ac.uk/efo/bubastis/)).\n* Separation of the sections of your html page so you can write them independently and replace only those needed.\n* Content negotiation and serialization of your ontology according to [W3C best practices](https://www.w3.org/TR/swbp-vocab-pub/)\n* Evaluation reports of your ontology (using the [OOPS! web service](https://oops.linkeddata.es/))\n* Integration with license metadata services ([Licensius](http://licensius.com/)) to automatically describe the license used in your ontology.\n"
+    ]
+  }
diff --git a/doc/metadataGuide/guide.md b/doc/metadataGuide/guide.md
@@ -92,16 +92,17 @@ We prioritize reusing metadata properties defined already. However, a small subs
 
 The table below summarizes all the metadata annotations recognized for ontology terms, in alphabetical order. Note that there are no `config.properties` annotations here, as these annotations are only read from the ontology file.
 
-|Metadata category |Ontology annotation property                     |Good practices document    |Accepted property value|Example          |
-|------------------|-------------------------------------------------|---------------------------|-----------------------|-----------------|
-|Definition        |[rdfs:comment], [skos:definition]                |[Sec 4.2] **[RECOMMENDED]**|[Text]                 |[ontology](#term)|
-|Deprecation status|[owl:deprecated]                                 |[Sec 4.5.1] **[OPTIONAL]** |[Boolean]              |[ontology](#term)|
-|Editorial note    |[skos:editorialNote]                             |N/A **[OPTIONAL]**         |[Text]                 |[ontology](#term)|
-|Example           |[vann:example], [skos:example]                   |[Sec 4.4] **[OPTIONAL]**   |[Text]                 |[ontology](#term)|
-|Label             |[rdfs:label], [skos:prefLabel], [obo:IAO_0000118]|[Sec 4.1] **[RECOMMENDED]**|[Text]                 |[ontology](#term)|
-|Original source   |[rdfs:isDefinedBy], [dc:source]                  |[Sec 4.3] **[OPTIONAL]**   |[URI]                  |[ontology](#term)|
-|Rationale         |[vaem:rationale]                                 |[Sec 4.6] **[OPTIONAL]**   |[Text]                 |[ontology](#term)|
-|Status            |[sw:term_status], [obo:IAO_0000114]              |[Sec 4.5.2] **[OPTIONAL]** |[Text]                 |[ontology](#term)|
+| Metadata category  | Ontology annotation property                      |Good practices document    |Accepted property value|Example          |
+|--------------------|---------------------------------------------------|---------------------------|-----------------------|-----------------|
+| Definition         | [rdfs:comment], [skos:definition]                 |[Sec 4.2] **[RECOMMENDED]**|[Text]                 |[ontology](#term)|
+| Deprecation status | [owl:deprecated]                                  |[Sec 4.5.1] **[OPTIONAL]** |[Boolean]              |[ontology](#term)|
+| Editorial note     | [skos:editorialNote]                              |N/A **[OPTIONAL]**         |[Text]                 |[ontology](#term)|
+| Example            | [vann:example], [skos:example]                    |[Sec 4.4] **[OPTIONAL]**   |[Text]                 |[ontology](#term)|
+| Label              | [rdfs:label], [skos:prefLabel], [obo:IAO_0000118] |[Sec 4.1] **[RECOMMENDED]**|[Text]                 |[ontology](#term)|
+| Original source    | [rdfs:isDefinedBy], [dc:source]                   |[Sec 4.3] **[OPTIONAL]**   |[URI]                  |[ontology](#term)|
+| Rationale          | [vaem:rationale]                                  |[Sec 4.6] **[OPTIONAL]**   |[Text]                 |[ontology](#term)|
+| Scope note         | [skos:scopeNote]                                  |N/A **[OPTIONAL]**         |[Text]                 |[ontology](#term)|
+| Status             | [sw:term_status], [obo:IAO_0000114]               |[Sec 4.5.2] **[OPTIONAL]** |[Text]                 |[ontology](#term)|
 
 
 ## <span id="onto">Example: Using ontology annotations (<a href="#table">Back to table</a>)
@@ -206,6 +207,7 @@ For status, the known values are: `unstable`, `testing`, `stable` and `archaic`
             sw:status "unstable";
             rdfs:isDefinedBy <https://w3id.org/example#> ;
             skos:editorialNote "Some editorial note by the creator of the term" ;
+            skos:scopeNote "A note that helps to clarify the meaning and/or the use of a concept" ;
             rdfs:label "Researcher"@en .
 ```
 
@@ -428,6 +430,7 @@ TurtleSerialization=ontology.ttl
 [skos:example]:                  http://www.w3.org/2004/02/skos/core#example
 [skos:note]:                     http://www.w3.org/2004/02/skos/core#note
 [skos:prefLabel]:                http://www.w3.org/2004/02/skos/core#prefLabel
+[skos:scopeNote]:                http://www.w3.org/2004/02/skos/core#scopeNote
 [sw:term_status]:                http://www.w3.org/2003/06/sw-vocab-status/ns#
 [vaem:rationale]:                http://www.linkedmodel.org/schema/vaem#rationale
 [vann:example]:                  http://purl.org/vocab/vann/example

diff --git a/src/main/resources/lode/cs.xml b/src/main/resources/lode/cs.xml
@@ -88,5 +88,6 @@
     <rangeIncludes>range includes</rangeIncludes>
     <usesRule>uses rule</usesRule>
     <editorialNote>redakční poznámka</editorialNote>
+    <scopeNote>poznámka k rozsahu</scopeNote>
     <externalproperty>externí vlastnosti</externalproperty>
 </labels>
diff --git a/src/main/resources/lode/de.xml b/src/main/resources/lode/de.xml
@@ -89,5 +89,6 @@
     <scenarios>Szenarien</scenarios>
     <usesRule>verwendet die Regel</usesRule>
     <editorialNote>redaktionelle Anmerkung</editorialNote>
+    <scopeNote>umfang Anmerkung</scopeNote>
     <externalproperty>externe Eigenschaft</externalproperty>
 </labels>
diff --git a/src/main/resources/lode/en.xml b/src/main/resources/lode/en.xml
@@ -88,6 +88,7 @@
     <domainIncludes>domain includes</domainIncludes>
     <rangeIncludes>range includes</rangeIncludes>
     <editorialNote>editorial note</editorialNote>
+    <scopeNote>scope note</scopeNote>
     <usedByRuleInAntecedent>used by rule (in antecedent)</usedByRuleInAntecedent>
     <usedByRuleInConsequent>used by rule (in consequent)</usedByRuleInConsequent>
     <externalproperty>external property</externalproperty>

diff --git a/src/main/resources/lode/es.xml b/src/main/resources/lode/es.xml
@@ -88,5 +88,6 @@
     <rangeIncludes>el rango incluye</rangeIncludes>
     <usesRule>utiliza regla</usesRule>
     <editorialNote>nota editorial</editorialNote>
+    <scopeNote>nota de alcance</scopeNote>
     <externalproperty>propiedad externa</externalproperty>
 </labels>
diff --git a/src/main/resources/lode/extraction.xsl b/src/main/resources/lode/extraction.xsl
@@ -1025,6 +1025,7 @@ http://www.oxygenxml.com/ns/doc/xsl ">
 
     <xsl:template name="get.entity.metadata">
         <xsl:call-template name="get.skos.editorial.note"/>
+        <xsl:call-template name="get.skos.scope.note"/>
         <xsl:call-template name="get.version"/>
         <xsl:call-template name="get.author"/>
         <xsl:call-template name="get.original.source"/>
@@ -2270,6 +2271,21 @@ http://www.oxygenxml.com/ns/doc/xsl ">
         </xsl:if>
     </xsl:template>
 
+    <xsl:template name="get.skos.scope.note">
+        <xsl:if test="exists(skos:scopeNote)">
+            <dl>
+                <dt>
+                    <xsl:value-of select="f:getDescriptionLabel('scopeNote')"/>
+                </dt>
+                <xsl:for-each select="skos:scopeNote">
+                    <dd>
+                        <xsl:value-of select="text()"/>
+                    </dd>
+                </xsl:for-each>
+            </dl>
+        </xsl:if>
+    </xsl:template>
+
     <xsl:template name="get.deprecated">
         <xsl:if test="exists(owl:deprecated)">
             <dl>

diff --git a/src/main/resources/lode/fr.xml b/src/main/resources/lode/fr.xml
@@ -88,4 +88,5 @@
     <rangeIncludes>cible comprend</rangeIncludes>
     <usesRule>utilise la règle</usesRule>
     <editorialNote>note éditoriale</editorialNote>
+    <scopeNote>note de portée</scopeNote>
 </labels>
diff --git a/src/main/resources/lode/it.xml b/src/main/resources/lode/it.xml
@@ -87,4 +87,5 @@
     <rangeIncludes>codominio include</rangeIncludes>
     <usesRule>usa la regola</usesRule>
     <editorialNote>nota redazionale</editorialNote>
+    <scopeNote>nota di scopo</scopeNote>
 </labels>
diff --git a/src/main/resources/lode/nl.xml b/src/main/resources/lode/nl.xml
@@ -87,4 +87,5 @@
     <rangeIncludes>bereik bevat</rangeIncludes>
     <usesRule>gebruikt regel</usesRule>
     <editorialNote>redactionele opmerking</editorialNote>
+    <scopeNote>scoop opmerking</scopeNote>
 </labels>
diff --git a/src/main/resources/widoco/de.properties b/src/main/resources/widoco/de.properties
@@ -5,7 +5,7 @@ previousVersion=Vorherige Version:
 revision=Revision:
 issued=Ausgestellt am:
 date=Release
-dateModified=Datum geändert:
+dateModified=&Auml;nderungsdatum:
 authors= Autoren:
 contributors=Beteiligte:
 extended=Erweiterte Ontologien:
@@ -21,23 +21,23 @@ nsText=</h3>\n<div id=\"ns\" align=\"center\">\n<table>\n<caption> <a href=\"#ns
 introTitle=Einf&uuml;hrung <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n
 introPlaceHolder=Einf&uuml;hrung <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<span class=\"markdown\">\nDies ist ein Platzhalter f&uuml;r die Einf&uuml;hrung. Die Einf&uuml;hrung sollte in kurzer Form die Ontologie und ihren Anwendungszweck beschreiben, sowie Informationen &uuml;ber ihren Entwicklungsstand und Kontext enthalten.</span>\n
 namespace=Deklaration der Namensr&auml;ume
-overviewTitle=&uuml;berblick
+overviewTitle=&Uuml;berblick
 overviewPlaceHolder=&uuml;berblick <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<span class=\"markdown\">\nDiese Ontologie beinhaltet die folgenden Klassen und Eigenschaften.</span>\n
 descriptionTitle=Beschreibung <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n
 descriptionPlaceHolder=Dies ist ein Platzhalter f&uuml;r die Beschreibung. Die Beschreibung sollte eine Erkl&auml;rung und Graphiken enthalten, die die Beziehung der Klassen untereinander und Anwendungsbeispiele enth&auml;lt.\n
-crossRefTitle=Querverweis f&uuml;r...
+crossRefTitle=Querverweis f&uuml;r
 crossRefTitle2=Klassen, Object Properties und Data Properties<span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span>
 crossRefPlaceHolder=Dieser Abschnitt enth&auml;lt Details f&uuml;r jede Klasse und jedes definierte Property, die definiert wurden durch
 classes=Klassen
-objProp=Object Properties
-dataProp=Data Properties
-extProp=External Properties
-annProp=Annotation Properties
-namedIndiv=Named Individuals
+objProp=Objekteigenschaften
+dataProp=Dateneigenschaften
+extProp=Externe Eigenschaften
+annProp=Anmerkungseigenschaften
+namedIndiv=Benannte Individuen
 referencesTitle=Referenzen
-referencesPlaceHolder=Referenzen <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<span class=\"markdown\">\nF&uuml;gen Sie Ihre Referenzen hier ein. &uuml;blicherweise wird dies in Form einer Liste gemacht.</span>\n
+referencesPlaceHolder=Referenzen <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<span class=\"markdown\">\nF&uuml;gen Sie Ihre Referenzen hier ein. &Uuml;blicherweise wird dies in Form einer Liste gemacht.</span>\n
 ackTitle=Danksagung
-ackText=Danksagung <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<p>\nDie Autoren bedanken sich bei<a href=\"http://www.essepuntato.it/\">Silvio Peroni</a> f&uuml;r die Entwicklung von <a href=\"http://www.essepuntato.it/lode\">LODE</a>, einer Umgebung zur Live-OWL-Dokumentation, die im Abschnitt Querverweise f&uuml;r die Darstellung verwendet wird, bei <a href=\"https://w3id.org/people/dgarijo\">Daniel Garijo</a> f&uuml;r die Entwicklung von <a href=\"https://github.com/dgarijo/Widoco\">Widoco</a>, welches f&uuml;r die Templates in dieser Anwendung verwendet wird.</p>\n</div>\n
+ackText=Danksagung <span class=\"backlink\"> zur&uuml;ck zum <a href=\"#toc\">Inhaltsverzeichnis</a></span></h2>\n<p>\nDie Autoren bedanken sich bei <a href=\"http://www.essepuntato.it/\">Silvio Peroni</a> f&uuml;r die Entwicklung von <a href=\"http://www.essepuntato.it/lode\">LODE</a>, einer Umgebung zur Live-OWL-Dokumentation, die im Abschnitt Querverweise f&uuml;r die Darstellung verwendet wird, bei <a href=\"https://w3id.org/people/dgarijo\">Daniel Garijo</a> f&uuml;r die Entwicklung von <a href=\"https://github.com/dgarijo/Widoco\">Widoco</a>, welches f&uuml;r die Templates in dieser Anwendung verwendet wird.</p>\n</div>\n
 prov1=Herkunft von
 prov2=Dokumentation
 createdBy=Entwickler der Ontologie:
@@ -69,12 +69,12 @@ addedDataProp=Hinzugef&uuml;gte Data Properties
 deletedDataProp=Gel&ouml;schte Data Properties
 added=Hinzugef&uuml;gt
 deleted=Gel&ouml;scht
-subClassOf=SubClass of
-subPropOf=SubProperty of
-domain=Domain
+subClassOf=Sub-Klasse von
+subPropOf=Super-Klasse von
+domain=Domäne
 range=Range
-unionOf=Union of
-intersectionOf=Intersection of
+unionOf=Vereinigung von
+intersectionOf=Schnittmenge von
 tableOfContents=Inhaltsverzeichnis
 compatible=Kompatibel mit
 incompatible=Inkompatibel mit

diff --git a/test/example_test.owl b/test/example_test.owl
@@ -108,6 +108,7 @@ xsd:date rdf:type rdfs:Datatype .
            rdfs:range :Researcher ;
            rdfs:comment "This example property indicates that an Organization has a Researcher as member"@en ;
            skos:editorialNote "banana in pajama"@en ;
+           skos:scopeNote "Use obj prop only for researchers in the specified organisation"@en ;
            rdfs:label "has member"@en .
 
 
@@ -144,6 +145,7 @@ xsd:date rdf:type rdfs:Datatype .
            rdfs:domain :Organization ;
            rdfs:range xsd:date ;
            skos:editorialNote "banana in pajama data prop"@en ;
+           skos:scopeNote "Use data prop only for researchers in the specified organisation"@en ;
            rdfs:comment "Date when an organization was founded"@en ;
            rdfs:label "founded in"@en .
 
@@ -163,6 +165,7 @@ xsd:date rdf:type rdfs:Datatype .
               <http://purl.org/vocab/vann/example> "University of Southern California"@en ;
               rdfs:comment "An organized body of people with a particular purpose, especially a business, society, association, etc."@en ;
               skos:editorialNote "SKOS note"@en ;
+              skos:scopeNote "Use this class for organisations"@en ;
               owl:equivalentClass <http://xmlns.com/foaf/0.1/Organization>;
               skos:prefLabel "organization";
               rdfs:isDefinedBy <https://w3id.org/example> ;