Merge pull request #687 from dgarijo/develop

Develop

doc/bestPractices/sections/checklist-en.html

@@ -23,7 +23,7 @@ <h5>Example:</h5>
 @prefix rdf: &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#&gt; .
 @prefix vann: &lt;http://purl.org/vocab/vann/&gt; .
 &lt;https://w3id.org/example&gt; rdf:type owl:Ontology ;
-	vann:preferredNamespaceUri "https://w3id.org/example" .
+	vann:preferredNamespaceUri &lt;https://w3id.org/example#&gt; .
 </pre>
 
 <h4 class="list" id="prefix">Prefix [<em class="rfc2119" title="RECOMMENDED">RECOMMENDED</em>]</h4>
@@ -593,6 +593,24 @@ <h5>Example:</h5>
     rdfs:seeAlso &lt;http://www.wikipathways.org/&gt; .
 </pre>
 
+<h3 id="code" class="list">Code repository (vocabulary maintenance) [<em class="rfc2119" title="OPTIONAL">OPTIONAL</em>]</h3>
+<p>
+Property used to indicate if there is a public code repository where the vocabulary is maintained. This information may be helpful to the adopter of your vocabulary, in order to raise issues and see current discussions.
+</p>
+
+<ul class="hlist"><strong>Properties you may use</strong>:
+	<li><a target="_blank" href="http://schema.org/codeRepository">schema:codeRepository</a> <strong>(PREFERRED)</strong></li>
+	<li><a target="_blank" href="http://usefulinc.com/ns/doap#repository">doap:repository</a></li>
+</ul>
+
+<h5>Example:</h5>
+<pre>
+@prefix owl: &lt;http://www.w3.org/2002/07/owl#&gt; .
+@prefix rdfs: &lt;http://www.w3.org/2000/01/rdf-schema#&gt; .
+&lt;http://vocabularies.wikipathways.org/wpTypes#&gt; a owl:Ontology ;
+    schema:codeRepository "https://github.com/user/repo"^^xsd:anyURI; .
+</pre>
+
 
 <h2 id="desc-term" class="list">Term checklist of metadata properties <span class="backlink"> back to <a href="#toc">ToC</a></span></h2>
 These metadata terms are targeted towards describing the classes, properties and data properties of the ontology. Adding them as part of the ontology is crucial for potential reusers:
@@ -698,7 +716,7 @@ <h5>Example:</h5>
 
 <h4 class="list" id="status1">Status [<em class="rfc2119" title="OPTIONAL">OPTIONAL</em>]</h4>
 <p>
-Property indicating the usage status of the term. For example, whether the term is mature enough, whether it has been deprecated, curated, etc. Note that some of the properties proposed below, such as obo:IAO_0000114, have as range a set of fixed values. The <a href="https://github.com/UKGovLD/registry-core/wiki/Principles-and-concepts#status-and-life-cycle">registry vocabulary</a> proposes a hierarchy of status that may be used to represent terms as well (reg:statusAccepted, reg:statusValid, reg:statusDeprecated, etc.).
+Property indicating the usage status of the term. For example, whether the term is mature enough, whether it has been deprecated, curated, etc. Note that some of the properties proposed below, such as obo:IAO_0000114, have as range a set of fixed values. The <a href="https://github.com/UKGovLD/registry-core/wiki/Principles-and-concepts#status-and-life-cycle">registry vocabulary</a> proposes a hierarchy of status that may be used to represent terms as well (reg:statusAccepted, reg:statusValid, reg:statusDeprecated, etc.). 
 </p>
 
 <ul class="hlist"><strong>Properties you may use</strong>:

doc/bestPractices/sections/introduction-en.html

@@ -71,7 +71,8 @@ <h2 id="conv" class="list">Properties summary</h2>
 <ul class="hlist" id="opt">
 	<li><a href="#abs">abstract</a></li>
 	<li><a href="#backwardCompatibility">backward compatibility</a></li>
-	<li><a href="#biblio">bibliographic Citation</a></li>
+	<li><a href="#biblio">bibliographic citation</a></li>
+	<li><a href="#code">code repository</a></li>
 	<li><a href="#diagram">diagram</a></li>
 	<li><a href="#doi">DOI</a></li>
 	<li><a href="#extended">extended Ontologies</a></li>
@@ -80,7 +81,7 @@ <h2 id="conv" class="list">Properties summary</h2>
 	<li><a href="#incompatibility">incompatibility</a></li>
 	<li><a href="#issuedDate">issued date</a></li>
 	<li><a href="#logo">logo</a></li>
-	<li><a href="#modificationDate">modification Date</a></li>
+	<li><a href="#modificationDate">modification date</a></li>
 	<li><a href="#publisher">publisher</a></li>
 	<li><a href="#similar">see also</a></li>
 	<li><a href="#source">source</a></li>

doc/configuration/config.properties

@@ -1,25 +1,27 @@
 
 abstract=An example ontology
-backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
-dateCreated="13 Nov, 2022"
-dateModified="15 Nov, 2022"
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
 authorsInstitution=First author institution;Second author institution
 authorsInstitutionURI=https://www.isi.edu/;https://www.isi.edu/
+citeAs="add some citation text here."
+backwardCompatibleWith=https://w3id.org/example/1.0.0
+codeRepository=https://github.com/dgarijo/example
 contributors=First contributor;Second contributor
 contributorsURI=http://example.org/contributor1;http://example.org/contributor2
 contributorsInstitution=First contributor institution;Second contributor institution
 contributorsInstitutionURI=https://isi.edu/;https://isi.edu/
+dateCreated="13 Nov, 2022"
+dateModified="15 Nov, 2022"
 description="A description of what the ontology does goes here"
 diagram="https://example.org/diagram.svg"
 DOI=
 funders=
-fundingGrants=
+funding=
 incompatibleWith=
-issued=
 images=image1.png;image2.png
+introduction="This is some introduction text"
+issued=
 licenseURI=http://creativecommons.org/licenses/by/2.0/
 licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
@@ -45,3 +47,5 @@ extendedOntologyURIs=http://example.org/test1; http://example.org/test2
 RDFXMLSerialization=ontology.xml
 TurtleSerialization=ontology.ttl
 NTSerialization=ontology.nt
+pathToOverview=overview.html
+pathToReferences=references.html

doc/configuration/configuration_doc.md

@@ -6,58 +6,63 @@ In order to have Widoco accept a configuration file, you need to create a `confi
 
 ```
 abstract=An example ontology
-backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
-dateCreated="13 Nov, 2022"
-dateIssued=
-dateModified="15 Nov, 2022"
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
 authorsInstitution=First author institution;Second author institution
 authorsInstitutionURI=https://www.isi.edu/;https://www.isi.edu/
+backwardCompatibleWith=https://w3id.org/example/1.0.0
+citeAs="add some citattion text here."
 contributors=First contributor;Second contributor
 contributorsURI=http://example.org/contributor1;http://example.org/contributor2
 contributorsInstitution=First contributor institution;Second contributor institution
 contributorsInstitutionURI=https://isi.edu/;https://isi.edu/
+dateCreated="13 Nov, 2022"
+dateIssued=
+dateModified="15 Nov, 2022"
 description="A description of what the ontology does goes here"
-diagram="https://example.org/diagram.svg"
 DOI=
 funder=
-fundingGrant=
+funding=
 incompatibleWith=
+introduction=A brief text for the introduction section may be written here.
 images=image1.png;image2.png
 licenseURI=http://creativecommons.org/licenses/by/2.0/
 licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
 logo="https://example.org/logo.svg"
 ontologyName=Example
-ontologyPrefix=exo
 ontologyNamespaceURI=https://w3id.org/example
+ontologyRevisionNumber=1.0.0
+ontologyTitle=The Example Ontology
+ontologyPrefix=exo
 previousVersionURI=https://w3id.org/example/1.0.0
 publisher=Ontology Engineering Group
 publisherURI=https://oeg-upm.es
 publisherInstitution=UPM
 publisherInstitutionURI=https://www.upm.es
 source=http://source1;http://source2
 seeAlso=http://firstResource
-ontologyTitle=The Example Ontology
 thisVersionURI=https://w3id.org/example/1.0.1
-ontologyRevisionNumber=v1.0.0
 status=Ontology Specification Draft
 ```
 
 Additional configuration options include the following
 ```
-importedOntologyNames=Imported Ontology 1; Imported Ontology 2
-importedOntologyURIs=http://example.org/test11; http://example.org/test22
+contextURI=JSON-LD context URI.
 extendedOntologyNames=test1; test2
 extendedOntologyURIs=http://example.org/test1; http://example.org/test2
+importedOntologyNames=Imported Ontology 1; Imported Ontology 2
+importedOntologyURIs=http://example.org/test11; http://example.org/test22
+pathToAbstract=abstract.html (superseedes abstract)
+pathToDescription=description.html (superseedes description)
+pathToIntro=intro.html (supersedes introduction)
+pathToOverview=overview.html
+pathToReferences=references.html 
+GoogleAnalyticsCode=UA-TestCodeGoesHere
+JSONLDSerialization=URL of the file with JSON-LD serialization. E.g., http://my-onto/onto.jsonld
+NTSerialization=URL of the file with N3 serialization. E.g., http://my-onto/onto.n3
 RDFXMLSerialization=URL of the file with RDF-XML serialization. E.g., http://my-onto/onto.owl
 TurtleSerialization=URL of the file with Turtle serialization. E.g., http://my-onto/onto..ttl;
-NTSerialization=URL of the file with N3 serialization. E.g., http://my-onto/onto.n3
-JSONLDSerialization=URL of the file with JSON-LD serialization. E.g., http://my-onto/onto.jsonld
-GoogleAnalyticsCode=UA-TestCodeGoesHere
-contextURI=JSON-LD context URI. 
 ```
 
 For more information, see the [Widoco readme options](https://github.com/dgarijo/Widoco/#options).

doc/configurationSamples/config/config.properties

@@ -1,7 +1,7 @@
 
 abstract=An example ontology
 backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
+citeAs="add some citation text here."
 creationDate="13 Nov, 2022"
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2

doc/metadataGuide/guide.md

@@ -45,9 +45,10 @@ The table below shows which ontology metadata annotations are recognized in WIDO
 |Abstract         |[dc:abstract], [dcterms:abstract]|abstract              |[Sec 3.2.4] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]|
 |Backwards compatible|[owl:backwardCompatibleWith]  |backwardCompatibleWith|[Sec 3.3.3] **[OPTIONAL]**|[URI] |[ontology](#onto), [config]|
 |Bibliographic citation|[dcterms:bibliographicCitation], [schema:citation]|citeAs|[Sec 3.6.2] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]|
+|Code repository|[schema:codeRepository], [doap:repository]|codeRepository|[Sec 3.10] **[OPTIONAL]**|[URI]|[ontology](#onto), [config]|
+|Contributors|[dcterms:contributor], [dc:contributor], [schema:contributor], [pav:contributedBy], [doap:documenter], [doap:maintainer], [doap:helper], [doap:translator]|contributors, contributorsURI, contributorsInstitution, contributorsInstitutionURI|[Sec 3.5.2] **[RECOMMENDED]**|[Text] or [Person] or [BNode]|[ontology](#onto), [config]|
 |Creation date|[dcterms:created], [schema:dateCreated], [prov:generatedAtTime], [pav:createdOn], [doap:created]|dateCreated|[Sec 3.4.2] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]|
 |Creators|[dcterms:creator], [dc:creator], [schema:creator], [pav:createdBy], [pav:authoredBy], [prov:wasAttributedTo], [doap:developer], [foaf:maker]|authors, authorsURI, authorsInstitution, authorsInstitutionURI|[Sec 3.5.1] **[RECOMMENDED]**|[Text] or [Person] or [BNode]|[ontology](#onto), [config]|
-|Contributors|[dcterms:contributor], [dc:contributor], [schema:contributor], [pav:contributedBy], [doap:documenter], [doap:maintainer], [doap:helper], [doap:translator]|contributors, contributorsURI, contributorsInstitution, contributorsInstitutionURI|[Sec 3.5.2] **[RECOMMENDED]**|[Text] or [Person] or [BNode]|[ontology](#onto), [config]|
 |Description|[dc:description], [dcterms:description], [schema:description], [rdfs:comment], [skos:note], [doap:description], [doap:shortdesc]|description|[Sec 3.2.3] **[OPTIONAL]**|[Text]|[ontology](#onto), [config]|
 |Diagram|[foaf:image], [foaf:depiction], [schema:image]|diagram   |[Sec 3.8.2] **[OPTIONAL]**|[Text]         |[ontology](#onto), [config]|
 |DOI    |[bibo:doi]                                    |DOI       |[Sec 3.6.1] **[OPTIONAL]**|[Text]         |[ontology](#onto), [config]|
@@ -140,6 +141,7 @@ The following `Turtle` code block shows sample annotations for each of the metad
     bibo:status <http://purl.org/ontology/bibo/status/draft> ;
     foaf:fundedBy <https://example.org/fundingOrganization> ;
     schema:funding <https://example.org/fundingGrant> ;
+    schema:codeRepository "https://github.com/dgarijo/example"^^xsd:anyURI;
     widoco:introduction "A paragraph with the introduction section of the documentation about your resource"@en ;
     widoco:rdfxmlSerialization "https://example.org/serialization/ontology.xml"^^xsd:anyURI ; 
     owl:versionInfo "1.0.1" .
@@ -212,27 +214,28 @@ Create a `config.properties` file and use the `-confFile` option to invoke Widoc
 
 ```
 abstract=An example ontology
-backwardCompatibleWith=https://w3id.org/example/1.0.0
-citeAs="add some citattion text here."
 authors=First Author;Second Author
 authorsURI=http://example.org/author1;http://example.org/author2
 authorsInstitution=First author institution;Second author institution
 authorsInstitutionURI=https://www.isi.edu/;https://www.isi.edu/
+backwardCompatibleWith=https://w3id.org/example/1.0.0
+citeAs="add some citattion text here."
+codeRepository=https://github.com/dgarijo/example
 contributors=First contributor;Second contributor
 contributorsURI=http://example.org/contributor1;http://example.org/contributor2
 contributorsInstitution=First contributor institution;Second contributor institution
 contributorsInstitutionURI=https://isi.edu/;https://isi.edu/
-description=A description of what the ontology does goes here
 dateCreated="13 Nov, 2022"
 dateIssued="14 Nov, 2022"
 dateModified="15 April, 2023"
-diagram="https://example.org/diagram.svg"
+description=A description of what the ontology does goes here
 extendedOntologyNames=test1; test2
 extendedOntologyURIs=http://example.org/test1; http://example.org/test2
 DOI=https://dx.doi.org/SOME/DOI
 funder=https://example.org/institution
 funding=https://example.org/fundingGrant
 incompatibleWith=https://w3id.org/example/0.0.1
+images=image1.png;image2.png
 importedOntologyNames=Imported Ontology 1; Imported Ontology 2
 importedOntologyURIs=http://example.org/test11; http://example.org/test22
 introduction=A brief text for the introduction section may be written here.
@@ -241,21 +244,28 @@ licenseName=CC-BY
 licenseIconURL=https://i.creativecommons.org/l/by/2.0/88x31.png
 logo="https://example.org/logo.svg"
 ontologyName=The Cohort Ontology
-ontologyPrefix=exo
 ontologyNamespaceURI=https://w3id.org/example
-previousVersionURI=https://w3id.org/example/1.0.0
-publisher=
-publisherURI=
-publisherInstitution=
-publisherInstitutionURI=
 ontologyTitle=The Example Ontology
+ontologyPrefix=exo
+ontologyRevisionNumber=1.0.0
+pathToAbstract=abstract.html (superseedes abstract)
+pathToDescription=description.html (superseedes description)
+pathToIntro=intro.html (supersedes introduction)
+pathToOverview=overview.html
+pathToReferences=references.html
+previousVersionURI=https://w3id.org/example/1.0.0
+publisher=Ontology Engineering Group
+publisherURI=https://oeg-upm.es
+publisherInstitution=UPM
+publisherInstitutionURI=https://www.upm.es
 thisVersionURI=https://w3id.org/example/1.0.1
-ontologyRevisionNumber=v1.0.0
+source=http://source1;http://source2
+seeAlso=http://firstResource
 status=Ontology Specification Draft
+JSONLDSerialization=ontology.nt
+NTSerialization=ontology.nt
 RDFXMLSerialization=ontology.xml
 TurtleSerialization=ontology.ttl
-NTSerialization=ontology.nt
-JSONLDSerialization=ontology.nt
 ```
 
 ## Glossary (<a href="#table">Back to table</a>)
@@ -309,6 +319,7 @@ JSONLDSerialization=ontology.nt
 [Sec 3.8.1]: https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#logo
 [Sec 3.8.2]: https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#diagram
 [Sec 3.9]:   https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#similar
+[Sec 3.10]:  https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#code
 [Sec 4.1]:   https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#label
 [Sec 4.2]:   https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#def
 [Sec 4.3]:   https://dgarijo.github.io/Widoco/doc/bestPractices/index-en.html#osource
@@ -351,6 +362,7 @@ JSONLDSerialization=ontology.nt
 [doap:maintainer]:               http://usefulinc.com/ns/doap#maintainer
 [doap:shortdesc]:                http://usefulinc.com/ns/doap#shortdesc
 [doap:translator]:               http://usefulinc.com/ns/doap#translator
+[doap:repository]:               http://usefulinc.com/ns/doap#repository
 [foaf:depiction]:                http://xmlns.com/foaf/0.1/depiction
 [foaf:family_name]:              http://xmlns.com/foaf/0.1/family_name
 [foaf:fundedBy]:                 http://xmlns.com/foaf/0.1/fundedBy
@@ -391,6 +403,7 @@ JSONLDSerialization=ontology.nt
 [schema:affiliation]:            https://schema.org/affiliation
 [schema:citation]:               https://schema.org/citation
 [schema:contributor]:            https://schema.org/contributor
+[schema:codeRepository]:         https://schema.org/codeRepository
 [schema:creator]:                https://schema.org/creator
 [schema:creativeWorkStatus]:     https://schema.org/creativeWorkStatus
 [schema:dateCreated]:            https://schema.org/dateCreated

src/main/java/lode/LODEGeneration.java

@@ -29,6 +29,7 @@
 import java.io.StringReader;
 import java.io.UnsupportedEncodingException;
 import java.net.URISyntaxException;
+import java.nio.charset.StandardCharsets;
 import java.util.HashSet;
 import java.util.Set;
 import javax.xml.transform.Transformer;
@@ -61,7 +62,7 @@ public static String getLODEhtml(Configuration c, File lodeResources) throws Exc
 
 			String content = "";
 			String lang = c.getCurrentLanguage();
-			if (lang == null || "".equals(lang)) {
+			if (lang == null || lang.isEmpty()) {
 				lang = "en";
 			}
 			// we have stored the ontology locally
@@ -318,7 +319,7 @@ private static String applyXSLTTransformation(String source, String ontologyUrl,
 
 		transformer.transform(inputSource, new StreamResult(output));
 
-		return output.toString("UTF-8").replace("any u r i", "anyURI");
+		return output.toString(StandardCharsets.UTF_8).replace("any u r i", "anyURI");
 	}
 
 }