Add ontology file and use it to replace the non existing describe

sib-swiss · Sep 25, 2024 · 68ad978 · 68ad978
1 parent fbb3a70
commit 68ad978
Show file tree

Hide file tree

Showing 6 changed files with 43 additions and 5 deletions.
diff --git a/.github/workflows/check.yml b/.github/workflows/check.yml
@@ -16,7 +16,7 @@ jobs:
         java-version: '21'
 
     - name: Install tester
-      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.0/sparql-examples-utils-2.0.0-uber.jar" -O sparql-examples-utils.jar
+      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.5/sparql-examples-utils-2.0.5-uber.jar" -O sparql-examples-utils.jar
 
     - name: Run tests
       run: java -jar sparql-examples-utils.jar test --input-directory=examples/
diff --git a/.github/workflows/publish_github_pages.yaml b/.github/workflows/publish_github_pages.yaml
@@ -32,7 +32,7 @@ jobs:
         java-version: '21'
 
     - name: Install tester
-      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.0/sparql-examples-utils-2.0.0-uber.jar" -O sparql-examples-utils-uber.jar
+      run: wget "https://github.com/sib-swiss/sparql-examples-utils/releases/download/v2.0.5/sparql-examples-utils-2.0.5-uber.jar" -O sparql-examples-utils-uber.jar
 
     - name: generate markdown
       run: java -jar sparql-examples-utils-uber.jar convert -i examples/ -m 

diff --git a/examples/HAMAP/2.ttl b/examples/HAMAP/2.ttl
@@ -3,10 +3,11 @@
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix spex: <https://purl.expasy.org/sparql-examples/ontology#> .
 
 ex:2 a sh:SPARQLExecutable ;
     rdfs:comment "Show the triples about <a href=\"https://hamap.expasy.org/rule/\">MF_00001</a>"^^rdf:HTML ;
-    sh:describe "DESCRIBE <http://purl.uniprot.org/hamap/MF_00001>" ;
+    spex:describe "DESCRIBE <http://purl.uniprot.org/hamap/MF_00001>" ;
     sh:prefixes _:sparql_examples_prefixes ;
     schema:target <https://hamap.expasy.org/sparql/> .
 
diff --git a/examples/UniProt/15_describe_an_EMBL_cds.ttl b/examples/UniProt/15_describe_an_EMBL_cds.ttl
@@ -2,9 +2,10 @@
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix spex: <https://purl.expasy.org/sparql-examples/ontology#> .
 
 ex:15 a sh:SPARQLExecutable ;
     rdfs:comment "Select all triples that relate to the EMBL CDS entry AA089367.1: "@en ;
-    sh:describe "DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>" ;
+    spex:describe "DESCRIBE <http://purl.uniprot.org/embl-cds/AAO89367.1>" ;
     schema:target <https://sparql.uniprot.org/sparql/> .
 
diff --git a/examples/UniProt/16_triples_about_species_human_in_taxonomy_graph.ttl b/examples/UniProt/16_triples_about_species_human_in_taxonomy_graph.ttl
@@ -3,11 +3,12 @@
 @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix schema: <https://schema.org/> .
 @prefix sh: <http://www.w3.org/ns/shacl#> .
+@prefix spex: <https://purl.expasy.org/sparql-examples/ontology#> .
 
 ex:16 a sh:SPARQLExecutable,
         sh:SPARQLSelectExecutable ;
     rdfs:comment "Select all triples that relate to the taxon that describes <i>Homo sapiens</i> in the named graph for <a href=\"http://sparql.uniprot.org/taxonomy\">taxonomy</a>"^^rdf:HTML ;
-    sh:describe """PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
+    spex:describe """PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
 
 DESCRIBE taxon:9606 
 FROM <http://sparql.uniprot.org/taxonomy>""" ;

diff --git a/examples/sparql-examples-ontology.ttl b/examples/sparql-examples-ontology.ttl
@@ -0,0 +1,35 @@
+# baseURI: https://purl.expasy.org/sparql-examples/ontology#
+
+@prefix spex:        <https://purl.expasy.org/sparql-examples/ontology#> .
+@prefix owl:     <http://www.w3.org/2002/07/owl#> .
+@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix sh:    	 <http://www.w3.org/ns/shacl#> .
+@prefix xsd:     <http://www.w3.org/2001/XMLSchema#> .
+
+<https://purl.expasy.org/sparql-examples/ontology#> a owl:Ontology ;
+	<http://purl.org/dc/terms/license>
+	<http://creativecommons.org/publicdomain/zero/1.0/> ;
+	owl:versionInfo "1.0"^^xsd:string .
+
+spex:describe 
+	a rdf:Property ;
+	rdfs:label "describe"@en ;
+	rdfs:comment "The SPARQL describe query to execute"@en ;
+	rdfs:domain spex:SPARQLDescribeExecutable ;
+	rdfs:range xsd:string ;
+	rdfs:isDefinedBy spex: .
+
+spex:SPARQLDescribeExecutable
+	a rdfs:Class ;
+	rdfs:label "SPARQL Describe executable"@en ;
+	rdfs:comment "The class of SPARQL executables that are based on Describe queries"@en ;
+	rdfs:subClassOf sh:SPARQLExecutable ;
+	rdfs:isDefinedBy spex: .
+
+spex:federatesWith
+	a rdf:Property ;
+	rdfs:label "Endpoint a SPARQL Executable uses with SERVICE clauses."@en ;
+	rdfs:range sh:SPARQLExecutable ;
+	rdfs:comment "SPARQL endpoints used in an SPARQL executable which are not the direct target."@en ;
+	rdfs:isDefinedBy spex: .