SPARQL queries

projects/project-2/assignment/GDC_lv6.sparql

@@ -0,0 +1,25 @@
+# checking whether all GDCs are generically depending on something
+#There is probably a conceptual mistake here, since this should be axioms and not direct connections between classes
+# lv 6
+
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?GDC (CONCAT("Warning: Generically Dependent Entity ", STR(?label), " doesn't generically depend on some entity.") AS ?warningMessage)
+WHERE {
+    #get all the subclasses of GDC
+    ?GDC rdfs:subClassOf+ obo:BFO_0000031 .
+    ?GDC rdfs:label ?label .
+    FILTER (!ISBLANK(?GDC)) .
+
+    # check whether it doesn't generically depend on something
+    FILTER NOT EXISTS {
+        ?GDC rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000084 ;
+            owl:someValuesFrom ?targetClass 
+        ].
+ }
+}

projects/project-2/assignment/OBO.sparql

@@ -0,0 +1,28 @@
+# Checks that no common OBO Foundry properties are used 
+# Level 5
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?subject ?predicate ?object
+WHERE {
+    ?subject ?predicate ?object .
+
+    FILTER (?predicate = obo:IAO_0000115 || 
+    ?predicate = obo:IAO_0000119 || 
+    ?predicate = obo:IAO_0000116 || 
+    ?predicate = obo:IAO_0000111 || 
+    ?predicate = obo:IAO_0000600 ||
+    ?predicate = obo:IAO_0010000 ||
+    ?predicate = obo:IAO_0000601 ||
+    ?predicate = obo:IAO_0000602 ||
+    ?predicate = obo:IAO_0000232
+    )
+
+    OPTIONAL {
+        ?predicate rdfs:label ?label .
+    }
+ BIND (CONCAT("Error: Property ", STR(?predicate), " is an OBO property.") AS ?errorMessage)
+
+}

projects/project-2/assignment/SDCs_lev6.sparql

@@ -0,0 +1,24 @@
+# Checking whether all SDCs are depending on some entity
+#There is probably a conceptual mistake here, since this should be axioms and not direct connections between classes
+# lev 6
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?SDC (CONCAT("Warning: Specifically Dependent Entity ", STR(?label), " doesn't specifically depend on some entity.") AS ?warningMessage)
+WHERE {
+    ?SDC rdfs:subClassOf+ obo:BFO_0000020 .
+    FILTER (!ISBLANK(?SDC)) .
+
+    FILTER NOT EXISTS {
+            ?subclass rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000195 ;
+            owl:someValuesFrom ?targetClass 
+        ].
+       }
+    OPTIONAL {
+        ?SDC rdfs:label ?label .
+    }
+}

projects/project-2/assignment/aristotelian_definition_level3.sparql

@@ -0,0 +1,29 @@
+
+# Find subjects with definitions
+# Get the parent class of the subject
+# Get the label of the parent class
+# Get the label of the subject 
+# Check whether the name of the parent class label appears in the definition, followed by that, who, where or inhering.
+# Suggested difficulty is level 3 (20 points)
+
+PREFIX cco: <http://www.ontologyrepository.com/CommonCoreOntologies/> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT ?subject ?parentClass ?definition ?subjectLabel ?error
+WHERE {
+    ?subject cco:definition ?definition .
+    ?subject rdfs:subClassOf ?parentClass .
+    ?parentClass rdfs:label ?parentClassLabel .
+    ?subject rdfs:label ?subjectLabel .
+
+    # Ensure subject is not blank
+    FILTER (!ISBLANK(?subject)) .
+
+    # Filter for non-Aristotelian definitions (that don't match the parent class label patterns)
+    FILTER NOT EXISTS {
+        FILTER(REGEX(LCASE(STR(?definition)), CONCAT(LCASE(STR(?parentClassLabel)), " (that|who|where|inhering)")))
+    } .
+
+    # Create the error message
+    BIND (concat("WARNING: Possible non-Aristotelian definition format for the following definition: ", str(?definition)) AS ?error)
+}

projects/project-2/assignment/inverse_property_lev4.sparql

@@ -0,0 +1,27 @@
+# Checking whether the object property has an inverse property or is the inverse property of a property.
+# This assumes we want to have inverses for all object properties
+# Level 4
+
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?property ?propertyLabel ?error
+WHERE {
+    # Find all object properties
+    ?property a owl:ObjectProperty .
+
+    # Check if the property does NOT have an inverse or is not the inverse of something else
+    FILTER (!ISBLANK (?property)) .
+    FILTER NOT EXISTS {
+        ?inverseproperty owl:inverseOf ?property .
+    }
+    FILTER NOT EXISTS {
+        ?property owl:inverseOf ?inverseproperty .
+    }
+    # Optional: get the label of the property
+
+    ?property rdfs:label ?propertyLabel .
+
+  FILTER regex(str(?property), "http://www.ontologyrepository.com/CommonCoreOntologies/")
+  BIND (concat("ERROR: There is no inverse property for the CCO property: ", str(?class)) AS ?error)
+}

projects/project-2/assignment/multiple_inheritance_l5.sparql

@@ -0,0 +1,21 @@
+#Check whether a class has more than on parent class
+#suggested difficulty level 5 (5 points)
+
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?subject ?error
+WHERE {
+    ?subject rdfs:subClassOf ?parentClass .
+
+    # Ensure that the subject is not blank
+    FILTER (!ISBLANK(?subject)) .
+    FILTER (!ISBLANK(?parentClass)) .
+
+    # Filter for classes within the CCO namespace
+    FILTER regex(str(?subject), "http://www.ontologyrepository.com/CommonCoreOntologies/")
+
+    # Create an error message
+    BIND (concat("ERROR: Class ", str(?subject), " has multiple parent classes: ", str(?parentClass)) AS ?error)
+}
+GROUP BY ?subject
+HAVING (COUNT(?parentClass) > 1)

projects/project-2/assignment/no_subclass_lv0.sparql

@@ -0,0 +1,21 @@
+#checking that classes are not subclasses of themselves
+# lv0
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT ?class ?warningMessage
+WHERE {
+    # Find all entities that have an axiom connecting them through BFO_0000199 to a subclass of BFO_0000148
+    ?classEntity a owl:Class
+
+    FILTER (!ISBLANK(?classEntity)) .
+
+    ?classEntity rdfs:subClassOf ?classEntity.
+
+    # Create a warning message
+    ?classEntity rdfs:label ?label .
+
+  BIND (CONCAT("Warning: Class ", STR(?label), " is a subclass of itself") AS ?warningMessage)
+}

projects/project-2/assignment/no_superclass_level5.sparql

@@ -0,0 +1,22 @@
+# checks if there are classes outside the BFO hierarchy
+#difficulty level 5 (5 points)
+
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?class ?label ?error
+WHERE {
+    # Find all classes in the ontology
+    ?class a owl:Class .
+    FILTER(?class != obo:BFO_0000001)
+    FILTER NOT EXISTS {
+        ?class rdfs:subClassOf ?superclass .
+    }
+    OPTIONAL {
+        ?class rdfs:label ?label .
+    }
+  FILTER (!ISBLANK (?class)) .
+  FILTER regex(str(?class), "http://www.ontologyrepository.com/CommonCoreOntologies/")
+  BIND (concat("ERROR: There is a class which is not in the BFO hierarchy ", str(?class)) AS ?error)
+}

projects/project-2/assignment/process_boundary_lev4.sparql

@@ -0,0 +1,31 @@
+#checks whether subclasses of process boundary are connected to a zero-dimensional temporal region
+#lev 4
+
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?entity ?warningMessage
+WHERE {
+    # Find all classes or subclasses of BFO_0000035
+    ?entity rdfs:subClassOf+ obo:BFO_0000035 .
+
+    # Ensure the target class is a subclass of zero-dimensional temporal region
+    ?targetClass rdfs:subClassOf* obo:BFO_0000148 .
+
+    # Check if they do NOT have the axiom connecting them through "occupies temporal region" to a subclass of zero-dimensional temporal region
+    FILTER NOT EXISTS {
+        ?entity rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000199 ;
+            owl:someValuesFrom ?targetClass
+        ] .
+    }
+
+    # Create a warning message
+    OPTIONAL {
+        ?entity rdfs:label ?label .
+    }
+    BIND(CONCAT("Warning: Class ", STR(COALESCE(?label, ?entity)), " is a process boundary but doesn't have occupy a zero-dimensional temporal region.") AS ?warningMessage)
+}

projects/project-2/assignment/realizations_lv6.sparql

@@ -0,0 +1,22 @@
+# This checks whether all the realizable entities are connected to a process through "has realization"
+# Level 6
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?subclass (CONCAT("Error: Realizable entity ", STR(?label), " doesn't have a process realizing it.") AS ?errorMessage)
+WHERE {
+    ?subclass rdfs:subClassOf+ obo:BFO_0000017 .
+    ?subclass rdfs:label ?label.
+    FILTER (!ISBLANK(?subclass)) .
+
+    FILTER NOT EXISTS {
+        ?subclass rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000054 ;
+            owl:someValuesFrom ?targetClass 
+        ].
+    }
+}

projects/project-2/assignment/reviewers/GDC_lv6.sparql

@@ -0,0 +1,24 @@
+# checking whether all GDCs are generically depending on something
+#There is probably a conceptual mistake here, since this should be axioms and not direct connections between classes
+# lv 6
+
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?GDC (CONCAT("Warning: Generically Dependent Entity ", STR(?label), " doesn't generically depend on some entity.") AS ?warningMessage)
+WHERE {
+    #get all the subclasses of GDC
+    ?GDC rdfs:subClassOf+ obo:BFO_0000031 .
+    ?GDC rdfs:label ?label .
+    FILTER (!ISBLANK(?GDC)) .
+
+    # check whether it doesn't generically depend on something
+    FILTER NOT EXISTS {
+        ?GDC rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000084 ;
+            owl:someValuesFrom ?targetClass 
+        ].
+}

projects/project-2/assignment/reviewers/OBO.sparql

@@ -0,0 +1,28 @@
+# Checks that no common OBO Foundry properties are used 
+# Level 5
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT DISTINCT ?subject ?predicate ?object
+WHERE {
+    ?subject ?predicate ?object .
+
+    FILTER (?predicate = obo:IAO_0000115 || 
+    ?predicate = obo:IAO_0000119 || 
+    ?predicate = obo:IAO_0000116 || 
+    ?predicate = obo:IAO_0000111 || 
+    ?predicate = obo:IAO_0000600 ||
+    ?predicate = obo:IAO_0010000 ||
+    ?predicate = obo:IAO_0000601 ||
+    ?predicate = obo:IAO_0000602 ||
+    ?predicate = obo:IAO_0000232
+    )
+
+    OPTIONAL {
+        ?predicate rdfs:label ?label .
+    }
+ BIND (CONCAT("Error: Property ", STR(?predicate), " is an OBO property.") AS ?errorMessage)
+
+}

projects/project-2/assignment/reviewers/SDCs_lev6.sparql

@@ -0,0 +1,24 @@
+# Checking whether all SDCs are depending on some entity
+#There is probably a conceptual mistake here, since this should be axioms and not direct connections between classes
+# lev 6
+
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX obo: <http://purl.obolibrary.org/obo/>
+
+SELECT ?SDC (CONCAT("Warning: Specifically Dependent Entity ", STR(?label), " doesn't specifically depend on some entity.") AS ?warningMessage)
+WHERE {
+    ?SDC rdfs:subClassOf+ obo:BFO_0000020 .
+    FILTER (!ISBLANK(?SDC)) .
+
+    FILTER NOT EXISTS {
+            ?subclass rdfs:subClassOf [
+            rdf:type owl:Restriction ;
+            owl:onProperty obo:BFO_0000195 ;
+            owl:someValuesFrom ?targetClass 
+        ].
+
+    OPTIONAL {
+        ?SDC rdfs:label ?label .
+    }
+}

projects/project-2/assignment/reviewers/aristotelian_definition_level3.sparql

@@ -0,0 +1,29 @@
+
+# Find subjects with definitions
+# Get the parent class of the subject
+# Get the label of the parent class
+# Get the label of the subject 
+# Check whether the name of the parent class label appears in the definition, followed by that, who, where or inhering.
+# Suggested difficulty is level 3 (20 points)
+
+PREFIX cco: <http://www.ontologyrepository.com/CommonCoreOntologies/> 
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
+
+SELECT ?subject ?parentClass ?definition ?subjectLabel ?error
+WHERE {
+    ?subject cco:definition ?definition .
+    ?subject rdfs:subClassOf ?parentClass .
+    ?parentClass rdfs:label ?parentClassLabel .
+    ?subject rdfs:label ?subjectLabel .
+
+    # Ensure subject is not blank
+    FILTER (!ISBLANK(?subject)) .
+
+    # Filter for non-Aristotelian definitions (that don't match the parent class label patterns)
+    FILTER NOT EXISTS {
+        FILTER(REGEX(LCASE(STR(?definition)), CONCAT(LCASE(STR(?parentClassLabel)), " (that|who|where|inhering)")))
+    } .
+
+    # Create the error message
+    BIND (concat("WARNING: Possible non-Aristotelian definition format for the following definition: ", str(?definition)) AS ?error)
+}

projects/project-2/assignment/reviewers/inverse_property_lev4.sparql

@@ -0,0 +1,27 @@
+# Checking whether the object property has an inverse property or is the inverse property of a property.
+# This assumes we want to have inverses for all object properties
+# Level 4
+
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT ?property ?propertyLabel ?error
+WHERE {
+    # Find all object properties
+    ?property a owl:ObjectProperty .
+
+    # Check if the property does NOT have an inverse or is not the inverse of something else
+    FILTER (!ISBLANK (?property)) .
+    FILTER NOT EXISTS {
+        ?inverseproperty owl:inverseOf ?property .
+    }
+    FILTER NOT EXISTS {
+        ?property owl:inverseOf ?inverseproperty .
+    }
+    # Optional: get the label of the property
+
+    ?property rdfs:label ?propertyLabel .
+
+  FILTER regex(str(?property), "http://www.ontologyrepository.com/CommonCoreOntologies/")
+  BIND (concat("ERROR: There is no inverse property for the CCO property: ", str(?class)) AS ?error)
+}