added queries from caseologue for testing in the control room

edamontology · May 24, 2024 · f5e0e87 · f5e0e87
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diff --git a/src/webapp/queries/end_dot_def_missing.rq b/src/webapp/queries/end_dot_def_missing.rq
@@ -0,0 +1,21 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?def ?label WHERE {
+   VALUES ?property {oboInOwl:hasDefinition}   
+   ?entity ?property ?def .
+   ?entity rdfs:label ?label .
+
+   FILTER NOT EXISTS {
+       FILTER REGEX(str(?def), "['.']+$")
+   }
+   FILTER (!isBlank(?def))
+
+}
+ORDER BY ?entity
+
diff --git a/src/webapp/queries/end_dot_label.rq b/src/webapp/queries/end_dot_label.rq
@@ -0,0 +1,19 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?value ?label WHERE {
+   VALUES ?property {rdfs:label}   
+   ?entity ?property ?value .
+   ?entity rdfs:label ?label .
+
+   FILTER REGEX(str(?value), "['.']+$")
+   FILTER (!isBlank(?entity))
+
+}
+ORDER BY ?entity
+
diff --git a/src/webapp/queries/end_space_annotation.rq b/src/webapp/queries/end_space_annotation.rq
@@ -0,0 +1,18 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?value ?label WHERE {
+   ?entity ?property ?value .
+   ?entity rdfs:label ?label .
+
+   FILTER REGEX(str(?value), "[\\s\r\n]+$")
+   FILTER (!isBlank(?entity))
+
+}
+ORDER BY ?entity
+
diff --git a/src/webapp/queries/eol_in_annotation.rq b/src/webapp/queries/eol_in_annotation.rq
@@ -0,0 +1,17 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?value ?label WHERE {
+   ?entity ?property ?value .
+   ?entity rdfs:label ?label .    
+   FILTER regex(?value, "\n")
+   FILTER (!isBlank(?entity))
+
+}
+ORDER BY ?entity
+
diff --git a/src/webapp/queries/get_uri.rq b/src/webapp/queries/get_uri.rq
@@ -0,0 +1,15 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?label WHERE {
+
+    ?entity a owl:Class .
+    OPTIONAL  {?entity rdfs:label ?label .}
+
+}
+ORDER BY ?entity
diff --git a/src/webapp/queries/literal_links.rq b/src/webapp/queries/literal_links.rq
@@ -0,0 +1,38 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?label ?value WHERE {
+    VALUES ?property {
+                    <http://edamontology.org/citation>
+                    <http://edamontology.org/documentation>
+                    <http://edamontology.org/information_standard>
+                    <http://edamontology.org/oldParent>
+                    <http://edamontology.org/ontology_used>
+                    <http://edamontology.org/organisation>
+                    <http://www.geneontology.org/formats/oboInOwl#consider>
+                    <http://www.geneontology.org/formats/oboInOwl#inSubset>
+                    <http://www.geneontology.org/formats/oboInOwl#replacedBy>
+                    <http://www.w3.org/2000/01/rdf-schema#seeAlso>
+                    <http://www.w3.org/2000/01/rdf-schema#subClassOf>
+                    <http://www.w3.org/2000/01/rdf-schema#subPropertyOf>
+                    <http://www.w3.org/2002/07/owl#annotatedProperty>
+                    <http://www.w3.org/2002/07/owl#inverseOf>
+                    <http://www.w3.org/2002/07/owl#disjointWith>
+                    <http://www.w3.org/2000/01/rdf-schema#domain>
+                    <http://www.w3.org/2000/01/rdf-schema#range>
+
+
+}
+
+?entity ?property ?value .
+
+FILTER isLiteral(?value) 
+?entity rdfs:label ?label .
+
+}
+ORDER BY ?entity
diff --git a/src/webapp/queries/mandatory_property_missing.rq b/src/webapp/queries/mandatory_property_missing.rq
@@ -0,0 +1,37 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?label ?property_subs_edam WHERE {
+
+    VALUES ?property {oboInOwl:hasDefinition
+                       edam:created_in
+                       #oboInOwl:inSubset
+                       rdfs:label
+                       rdfs:subClassOf }
+    ?entity a owl:Class .
+
+    FILTER NOT EXISTS {?entity owl:deprecated true .}
+    OPTIONAL {?entity rdfs:label ?label .}
+    FILTER ( ?entity != <http://edamontology.org/data_0006>)
+    FILTER ( ?entity != <http://edamontology.org/topic_0003>)
+    FILTER ( ?entity != <http://www.w3.org/2002/07/owl#DeprecatedClass>)
+    FILTER ( ?entity != <http://edamontology.org/operation_0004>)
+    FILTER ( ?entity != <http://edamontology.org/format_1915>)
+
+    FILTER NOT EXISTS {?entity ?property ?value .
+                       MINUS { ?value rdf:type owl:Restriction .} #to prevent concept with rdfs:subClassOf property being only restriction (e.g. has_topic)
+                       }
+    FILTER (!isBlank(?entity))
+    # UNION
+    # {
+    # VALUES ?property { oboInOwl:inSubset
+    #                     }
+    # FILTER NOT EXISTS {?entity ?property <http://purl.obolibrary.org/obo/edam#edam> .}
+    # }
+}
+ORDER BY ?entity
diff --git a/src/webapp/queries/start_space_annotation.rq b/src/webapp/queries/start_space_annotation.rq
@@ -0,0 +1,18 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?value ?label WHERE {
+   ?entity ?property ?value .
+   ?entity rdfs:label ?label .        
+   FILTER REGEX(str(?value), "^[\\s\r\n]+")
+   FILTER (!isBlank(?entity))
+
+}
+ORDER BY ?entity
+
+
diff --git a/src/webapp/queries/tab_in_annotation.rq b/src/webapp/queries/tab_in_annotation.rq
@@ -0,0 +1,20 @@
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX oboInOwl: <http://www.geneontology.org/formats/oboInOwl#>
+PREFIX edam:<http://edamontology.org/>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+
+SELECT DISTINCT ?entity ?property ?value ?label WHERE {
+   ?entity ?property ?value .
+   ?entity rdfs:label ?label .        
+
+   FILTER regex(?value, "\t")
+   FILTER (!isBlank(?entity))
+
+}
+ORDER BY ?entity
+
+
+