Merge 8387c83 into 3f35b38

CHANGELOG.md

@@ -26,6 +26,7 @@ This changelog was started for release 4.2.0.
 - Store 'version' value when storing results. Not used for now, but might be used in deprecation warnings later
 - Removed some lines from coverage computation
 - Added 'indirect relations': Two entities will be linked on the graph, without a direct relation between them (same as faldo relations). This is intended to be used with 'linked attributes' (ex: get all entities B where B.color is the same as A.color, without a direct relation between A and B)
+- Basic support for 'skos:broader' and 'skos:narrower' for ontologies.
 
 ### Fixed
 

askomics/libaskomics/RdfFile.py

@@ -79,10 +79,13 @@ def get_preview(self):
                 head += ttl_file.readline()
 
         location = None
+        remote_graph = None
         try:
             location, remote_graph = self.get_location_and_remote_graph()
         except Exception as e:
             self.error_message = str(e)
+            # Todo: Better error management
+            raise e
 
         return {
             'type': self.type,

askomics/react/src/routes/query/ontolinkview.jsx

@@ -16,6 +16,28 @@ export default class OntoLinkView extends Component {
 
 
   render () {
+
+    let content = (
+      <>
+        <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf">children of</option>
+        <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf*">descendants of</option>
+        <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf">parents of</option>
+        <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf*">ancestors of</option>
+      </>
+    )
+
+    if (this.props.link.uri.includes("http://www.w3.org/2004/02/skos/core")){
+      content = (
+        <>
+          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#broader' ? true : false} value="http://www.w3.org/2004/02/skos/core#broader">children of</option>
+          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#broader*' ? true : false} value="http://www.w3.org/2004/02/skos/core#broader*">descendants of</option>
+          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#narrower' ? true : false} value="http://www.w3.org/2004/02/skos/core#narrower">parents of</option>
+          <option selected={this.props.link.uri == 'http://www.w3.org/2004/02/skos/core#narrower*' ? true : false} value="http://www.w3.org/2004/02/skos/core#narrower*">ancestors of</option>
+        </>
+      )
+    }
+
+
     return (
       <div className="container">
         <h5>Ontological Relation</h5>
@@ -25,10 +47,7 @@ export default class OntoLinkView extends Component {
           <tr>
             <td>
              <CustomInput type="select" id={this.props.link.id} name="ontology_position" onChange={this.handleChangeOntologyType}>
-                <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf">children of</option>
-                <option selected={this.props.link.uri == 'http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="http://www.w3.org/2000/01/rdf-schema#subClassOf*">descendants of</option>
-                <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf">parents of</option>
-                <option selected={this.props.link.uri == '^http://www.w3.org/2000/01/rdf-schema#subClassOf*' ? true : false} value="^http://www.w3.org/2000/01/rdf-schema#subClassOf*">ancestors of</option>
+              {content}
               </CustomInput>
             </td>
             <td>&nbsp;a term</td>

askomics/react/src/routes/query/query.jsx

@@ -1548,10 +1548,15 @@ export default class Query extends Component {
 
   getOntoLabel (uri) {
       let labels = {}
-      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is children of"
+      labels["http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is child of"
       labels["http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "is descendant of"
-      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is parents of"
+      labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf"] = "is parent of"
       labels["^http://www.w3.org/2000/01/rdf-schema#subClassOf*"] = "is ancestor of"
+
+      labels["http://www.w3.org/2004/02/skos/core#broader"] = "is child of"
+      labels["http://www.w3.org/2004/02/skos/core#broader*"] = "is descendant of"
+      labels["http://www.w3.org/2004/02/skos/core#narrower"] = "is parent of"
+      labels["http://www.w3.org/2004/02/skos/core#narrower*"] = "is ancestor of"
       return labels[uri]
   }
 

docs/abstraction.md

@@ -274,6 +274,10 @@ Ontologies needs to be are defined as follows:
 
 You will then need to add any relations and attributes using blank nodes:
 
+!!! warning
+    If using "skos:narrower" or "skos:broader", you only need to define one of them.
+    AskOmics will show both options in the UI
+
 ```turtle
 # SubCLassOf relation
 _:blank1 a askomics:AskomicsRelation .
@@ -304,6 +308,9 @@ Here is an example of an ontological class:
 <class_uri> skos:prefLabel "OntologyLabel" .
 ```
 
+!!! warning
+    For now, AskOmics expect the classes to be defined by 'owl:Class'
+
 !!! note "Info"
     The label does not need to be `rdfs:label`, but you will need to specify the correct label in the UI.