#4463 - Add human phenotype ontology knowledge base profile

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/yaml/KnowledgeBaseInfo.java

@@ -37,7 +37,13 @@ public class KnowledgeBaseInfo
     private String authorName;
 
     @JsonProperty("website-url")
-    private String websiteURL;
+    private String websiteUrl;
+
+    @JsonProperty("license-name")
+    private String licenseName;
+
+    @JsonProperty("license-url")
+    private String licenseUrl;
 
     public String getDescription()
     {
@@ -69,14 +75,34 @@ public void setAuthorName(String aAuthorName)
         authorName = aAuthorName;
     }
 
-    public String getWebsiteURL()
+    public String getWebsiteUrl()
+    {
+        return websiteUrl;
+    }
+
+    public void setWebsiteUrl(String aWebsiteURL)
+    {
+        websiteUrl = aWebsiteURL;
+    }
+
+    public String getLicenseName()
+    {
+        return licenseName;
+    }
+
+    public void setLicenseName(String aLicenseName)
+    {
+        licenseName = aLicenseName;
+    }
+
+    public String getLicenseUrl()
     {
-        return websiteURL;
+        return licenseUrl;
     }
 
-    public void setWebsiteURL(String aWebsiteURL)
+    public void setLicenseUrl(String aLicenseUrl)
     {
-        websiteURL = aWebsiteURL;
+        licenseUrl = aLicenseUrl;
     }
 
     @Override
@@ -92,12 +118,15 @@ public boolean equals(Object o)
         return Objects.equals(description, that.description)
                 && Objects.equals(hostInstitutionName, that.hostInstitutionName)
                 && Objects.equals(authorName, that.authorName)
-                && Objects.equals(websiteURL, that.websiteURL);
+                && Objects.equals(websiteUrl, that.websiteUrl)
+                && Objects.equals(licenseName, that.licenseName)
+                && Objects.equals(licenseUrl, that.licenseUrl);
     }
 
     @Override
     public int hashCode()
     {
-        return Objects.hash(description, hostInstitutionName, authorName, websiteURL);
+        return Objects.hash(description, hostInstitutionName, authorName, websiteUrl, licenseName,
+                licenseUrl);
     }
 }

inception/inception-kb/src/main/java/de/tudarmstadt/ukp/inception/kb/yaml/KnowledgeBaseProfile.java

@@ -17,13 +17,12 @@
  */
 package de.tudarmstadt.ukp.inception.kb.yaml;
 
+import static java.nio.charset.StandardCharsets.UTF_8;
 import static java.util.Collections.emptyList;
 
 import java.io.IOException;
 import java.io.InputStreamReader;
-import java.io.Reader;
 import java.io.Serializable;
-import java.nio.charset.StandardCharsets;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
@@ -217,9 +216,9 @@ public void setDefaultDataset(String aDefaultDataset)
 
     public static Map<String, KnowledgeBaseProfile> readKnowledgeBaseProfiles() throws IOException
     {
-        try (Reader r = new InputStreamReader(
+        try (var r = new InputStreamReader(
                 KnowledgeBaseProfile.class.getResourceAsStream(KNOWLEDGEBASE_PROFILES_YAML),
-                StandardCharsets.UTF_8)) {
+                UTF_8)) {
             ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
             return mapper.readValue(r, new TypeReference<HashMap<String, KnowledgeBaseProfile>>()
             {

inception/inception-kb/src/main/resources/de/tudarmstadt/ukp/inception/kb/yaml/knowledgebase-profiles.yaml

@@ -38,7 +38,7 @@ babel_net:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       BabelNet is a multilingual lexicalized semantic network and ontology that was automatically 
       created by linking Wikipedia to WordNet.
     host-institution-name: Linguistic Computing Laboratory at Sapienza University of Rome
@@ -64,7 +64,7 @@ db_pedia:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       DBpedia is a crowd-sourced community effort to extract structured content from the information 
       created in various Wikimedia projects.
     host-institution-name: Leipzig University, University of Mannheim, OpenLink Software
@@ -92,7 +92,7 @@ wikidata:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.wikidata.org/prop/direct/P1647
   info:
-    description: > 
+    description: |
       Wikidata is a free and open knowledge base and acts as central storage for the structured data
       of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wikisource, and others.
     host-institution-name: Wikimedia Foundation, Inc.
@@ -147,7 +147,7 @@ zbw-stw-economics:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       Thesaurus that provides vocabulary on any economic subject. Almost 6,000 standardized subject
       headings and about 20,000 additional entry terms to support individual keywords.
     host-institution-name: ZBW - Leibniz Information Centre for Economics
@@ -173,7 +173,7 @@ zbw-gnd:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       Mapping Integrated Authority File (GND).The Integrated Authority File (GND) is a controlled 
       keyword system, that is mainly used for indexing in German libraries.
     host-institution-name: ZBW - Leibniz Information Centre for Economics
@@ -251,7 +251,7 @@ wine_ontology:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       An example OWL ontology. Derived from the DAML Wine ontology at 
       http://ontolingua.stanford.edu/doc/chimaera/ontologies/wines.daml
     host-institution-name: "-"
@@ -277,9 +277,66 @@ olia_penn.owl:
     property-description: http://www.w3.org/2000/01/rdf-schema#comment
     subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
   info:
-    description: >
+    description: |
       Ontologies of Linguistic Annotation (OLiA)
     host-institution-name: Applied Computational Linguistics (ACoLi) Lab at the Goethe University Frankfurt, Germany
     author-name: Christian Chiarcos and Maria Sukhareva
     website-url: http://www.acoli.informatik.uni-frankfurt.de/resources/olia/
-
+
+iao:
+  name: Information Artifact Ontology (IAO) (v2022-11-07)
+  type: LOCAL
+  default-language: en
+  reification: NONE
+  access:
+    access-url: https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2022-11-07/iao.owl
+    full-text-search: http://www.openrdf.org/contrib/lucenesail#matches
+  mapping:
+    class: http://www.w3.org/2000/01/rdf-schema#Class
+    subclass-of: http://www.w3.org/2000/01/rdf-schema#subClassOf
+    instance-of: http://www.w3.org/1999/02/22-rdf-syntax-ns#type
+    label: http://www.w3.org/2000/01/rdf-schema#label
+    property-type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
+    description: http://www.w3.org/2000/01/rdf-schema#comment
+    property-label: http://www.w3.org/2000/01/rdf-schema#label
+    property-description: http://www.w3.org/2000/01/rdf-schema#comment
+    subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
+  info:
+    description: |
+      The Information Artifact Ontology (IAO) is a new ontology of information entities, originally driven by work by 
+      the OBI digital entity and realizable information entity branch.
+
+      For more information, please refer to the project's website.
+    website-url: https://github.com/information-artifact-ontology/IAO/
+
+hpo-2024-01-16:
+  name: Human Phenotype Ontology (v2024-01-16)
+  type: LOCAL
+  default-language: en
+  reification: NONE
+  access:
+    access-url: https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2024-01-16/hp-full.owl
+    full-text-search: http://www.openrdf.org/contrib/lucenesail#matches
+  mapping:
+    class: http://www.w3.org/2002/07/owl#Class
+    subclass-of: http://www.w3.org/2000/01/rdf-schema#subClassOf
+    instance-of: http://www.w3.org/1999/02/22-rdf-syntax-ns#type
+    description: http://purl.obolibrary.org/obo/IAO_0000115
+    label: http://www.w3.org/2000/01/rdf-schema#label
+    property-type: http://www.w3.org/1999/02/22-rdf-syntax-ns#Property
+    subproperty-of: http://www.w3.org/2000/01/rdf-schema#subPropertyOf
+    property-label: http://www.w3.org/2000/01/rdf-schema#label
+    property-description: http://www.w3.org/2000/01/rdf-schema#comment
+  additional-matching-properties:
+    - http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
+  info:
+    description: |
+      The Human Phenotype Ontology (HPO) project provides an ontology of medically relevant phenotypes, 
+      disease-phenotype annotations, and the algorithms that operate on these. 
+
+      This resources is quite large. Downloading and importing it may take some time.
+
+       Find out more at [http://www.human-phenotype-ontology.org](http://www.human-phenotype-ontology.org).
+    host-institution-name: The Jackson Laboratory 
+    website-url: https://hpo.jax.org/app/
+    license-url: https://hpo.jax.org/app/license

inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/KnowledgeBaseProfileDeserializationTest.java

@@ -87,7 +87,7 @@ private KnowledgeBaseInfo createReferenceInfo()
         referenceInfo.setDescription(description);
         referenceInfo.setAuthorName(author);
         referenceInfo.setHostInstitutionName(host);
-        referenceInfo.setWebsiteURL(website);
+        referenceInfo.setWebsiteUrl(website);
         return referenceInfo;
     }
 

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/KnowledgeBaseInfoPanel.html

@@ -39,11 +39,23 @@
       </label>
       <label wicket:id="authorName" class="col-sm-9 text-muted" style="font-weight: normal;"></label>
     </div>
-    <div class="row form-row" wicket:enclosure="websiteURL">
+    <div class="row form-row" wicket:enclosure="websiteUrl">
       <label class="col-form-label col-sm-3">
         <wicket:message key="kb.wizard.steps.accessSpecific.homepage" />
       </label>
-      <a wicket:id="websiteURL" class="col-sm-9" target="_blank"></a>
+      <div class="col-sm-9">
+        <a wicket:id="websiteUrl" target="_blank"></a>
+        <i class="fas fa-external-link-alt text-secondary"></i>
+      </div>
+    </div>
+    <div class="row form-row" wicket:enclosure="licenseUrl">
+      <label class="col-form-label col-sm-3">
+        <wicket:message key="kb.wizard.steps.accessSpecific.license" />
+      </label>
+      <div class="col-sm-9">
+        <a wicket:id="licenseUrl" target="_blank"></a>
+        <i class="fas fa-external-link-alt text-secondary"></i>
+      </div>
     </div>
   </wicket:panel>
 </body>

inception/inception-ui-kb/src/main/java/de/tudarmstadt/ukp/inception/ui/kb/project/KnowledgeBaseInfoPanel.java

@@ -19,6 +19,7 @@
 
 import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.wicket.markup.html.basic.Label;
 import org.apache.wicket.markup.html.link.ExternalLink;
 import org.apache.wicket.markup.html.panel.Panel;
@@ -36,13 +37,26 @@ public KnowledgeBaseInfoPanel(String aId, CompoundPropertyModel<KnowledgeBaseInf
     {
         super(aId, aModel);
 
-        queue(new MarkdownLabel("description", aModel.bind("description"))
-                .add(visibleWhen(() -> aModel.getObject() != null)));
-        queue(new Label("hostInstitutionName", aModel.bind("hostInstitutionName"))
-                .add(visibleWhen(() -> aModel.getObject() != null)));
-        queue(new Label("authorName", aModel.bind("authorName"))
-                .add(visibleWhen(() -> aModel.getObject() != null)));
-        queue(new ExternalLink("websiteURL", aModel.bind("websiteURL"), aModel.bind("websiteURL"))
-                .add(visibleWhen(() -> aModel.getObject() != null)));
+        var description = aModel.map(KnowledgeBaseInfo::getDescription);
+        queue(new MarkdownLabel("description", description)
+                .add(visibleWhen(description.map(StringUtils::isNotBlank))));
+
+        var hostInstitutionName = aModel.map(KnowledgeBaseInfo::getHostInstitutionName);
+        queue(new Label("hostInstitutionName", hostInstitutionName)
+                .add(visibleWhen(hostInstitutionName.map(StringUtils::isNotBlank))));
+
+        var authorName = aModel.map(KnowledgeBaseInfo::getAuthorName);
+        queue(new Label("authorName", authorName)
+                .add(visibleWhen(authorName.map(StringUtils::isNotBlank))));
+
+        var websiteURL = aModel.map(KnowledgeBaseInfo::getWebsiteUrl);
+        queue(new ExternalLink("websiteUrl", websiteURL, websiteURL)
+                .add(visibleWhen(websiteURL.map(StringUtils::isNotBlank))));
+
+        var licenseUrl = aModel.map(KnowledgeBaseInfo::getLicenseUrl);
+        var licenseName = aModel.map(KnowledgeBaseInfo::getLicenseName)
+                .orElseGet(licenseUrl::getObject);
+        queue(new ExternalLink("licenseUrl", licenseUrl, licenseName)
+                .add(visibleWhen(licenseUrl.map(StringUtils::isNotBlank))));
     }
 }