Basic script to compare ontologies

.gitignore

+env/*

examples/compare_ontologies.py

+#!/usr/bin/python3.10
+# -*-coding:Utf-8 -*
+
+#==============================================================================
+# ontoScorer: Script to compare two ontologies and calculate metrics 
+#------------------------------------------------------------------------------
+# This script loads two OWL ontologies from local files, extracts classes from 
+# these ontologies and compares them. It then calculates precision, recall, and
+# F1 score, which are commonly used metrics in information retrieval to assess 
+# the quality of a retrieval system. The paths to the ontology files are 
+# specified directly in the script.
+#==============================================================================
+
+from rdflib import Graph, OWL
+from rdflib.namespace import split_uri
+from sklearn.metrics import precision_score, recall_score, f1_score
+
+# Define the path to the data folder
+DATA_FOLDER_PATH = "data"
+
+# Define paths to the ontology files
+REFERENCE_ONTOLOGY_PATH = f"{DATA_FOLDER_PATH}/reference_ontology.ttl"
+GENERATED_ONTOLOGY_PATH = f"{DATA_FOLDER_PATH}/generated_ontology.ttl"
+
+
+#==============================================================================
+# Methods to manipulate ontologies and calculate the metrics
+#==============================================================================  
+
+def load_ontology(path):
+    g = Graph()
+    g.parse(path, format="ttl")
+    return g
+
+
+def get_classes(ontology, ontology_path):
+    classes = set()
+    triplets_count = 0
+    for s, p, o in ontology.triples((None, None, None)):
+        triplets_count += 1
+        if o == OWL.Class:
+            _, class_name = split_uri(s)
+            classes.add(class_name)
+    print(f"Ontology analyzed: {ontology_path}")
+    print(f"Number of classes found: {len(classes)}")
+    print(f"Number of triplets analyzed: {triplets_count}")
+    return classes
+
+
+def calculate_metrics(reference_classes, generated_classes):
+    all_classes = reference_classes.union(generated_classes)
+    y_true = [1 if cls in reference_classes else 0 for cls in all_classes]
+    y_pred = [1 if cls in generated_classes else 0 for cls in all_classes]
+
+    precision = precision_score(y_true, y_pred)
+    recall = recall_score(y_true, y_pred)
+    f1 = f1_score(y_true, y_pred)
+
+    return precision, recall, f1
+
+
+#==============================================================================
+# Main Method
+#==============================================================================  
+
+def main():
+    # Load ontologies
+    ref_ontology = load_ontology(REFERENCE_ONTOLOGY_PATH)
+    gen_ontology = load_ontology(GENERATED_ONTOLOGY_PATH)
+
+    # Extract classes
+    ref_classes = get_classes(ref_ontology, REFERENCE_ONTOLOGY_PATH)
+    gen_classes = get_classes(gen_ontology, GENERATED_ONTOLOGY_PATH)
+
+    # Calculate metrics
+    precision, recall, f1 = calculate_metrics(ref_classes, gen_classes)
+
+    # Print results
+    print(f"Precision: {precision}")
+    print(f"Recall: {recall}")
+    print(f"F1 Score: {f1}")
+
+if __name__ == "__main__":
+    main()
+

examples/data/generated_ontology.ttl

+@prefix ns1: <https://tenet.tetras-libre.fr/base-ontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+<https://tenet.tetras-libre.fr/extract-result#SolarSystem> a owl:Individual,
+        <https://tenet.tetras-libre.fr/extract-result#system>,
+        <https://tenet.tetras-libre.fr/extract-result#system-hasPart-object>,
+        <https://tenet.tetras-libre.fr/extract-result#system-hasPart-sun> ;
+    rdfs:label "SolarSystem" ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#direct> a owl:ObjectProperty ;
+    rdfs:label "direct" ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#gravitation-bind-system> a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty <https://tenet.tetras-libre.fr/extract-result#bind> ;
+            owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#system> ],
+        <https://tenet.tetras-libre.fr/extract-result#gravitation> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#hasManner> a owl:ObjectProperty ;
+    rdfs:label "hasManner" ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#not-direct> a owl:ObjectProperty ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object-orbit-hasManner-direct-sun> a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty <https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-direct> ;
+            owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+        <https://tenet.tetras-libre.fr/extract-result#object> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object-orbit-hasManner-not-direct-sun> a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty <https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-not-direct> ;
+            owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+        <https://tenet.tetras-libre.fr/extract-result#object> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#bind> a owl:ObjectProperty ;
+    rdfs:label "bind" ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#gravitation> a owl:Class ;
+    rdfs:label "gravitation" ;
+    rdfs:subClassOf ns1:Entity ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-direct> a owl:ObjectProperty ;
+    rdfs:subPropertyOf <https://tenet.tetras-libre.fr/extract-result#orbit> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit-hasManner-not-direct> a owl:ObjectProperty ;
+    rdfs:subPropertyOf <https://tenet.tetras-libre.fr/extract-result#orbit> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system-hasPart-object> a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty <https://tenet.tetras-libre.fr/extract-result#hasPart> ;
+            owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#object> ],
+        <https://tenet.tetras-libre.fr/extract-result#system> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system-hasPart-sun> a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty <https://tenet.tetras-libre.fr/extract-result#hasPart> ;
+            owl:someValuesFrom <https://tenet.tetras-libre.fr/extract-result#sun> ],
+        <https://tenet.tetras-libre.fr/extract-result#system> ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#hasPart> a owl:ObjectProperty ;
+    rdfs:label "hasPart" ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#orbit> a owl:ObjectProperty ;
+    rdfs:label "orbit" ;
+    rdfs:subPropertyOf ns1:Out_ObjectProperty ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#object> a owl:Class ;
+    rdfs:label "object" ;
+    rdfs:subClassOf ns1:Entity ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#sun> a owl:Class ;
+    rdfs:label "sun" ;
+    rdfs:subClassOf ns1:Entity ;
+    ns1:fromStructure "unknown" .
+
+<https://tenet.tetras-libre.fr/extract-result#system> a owl:Class ;
+    rdfs:label "system" ;
+    rdfs:subClassOf ns1:Entity,
+        ns1:Undetermined_Thing ;
+    ns1:fromStructure "unknown" .
+

examples/data/reference_ontology.ttl

+@prefix base: <https://reference.tetras-libre.fr/base-ontology#> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix result: <https://reference.tetras-libre.fr/expected-result#> .
+
+result:SolarSystem a owl:Individual,
+        result:system,
+        result:system-isBindBy-gravitation,
+        result:system-hasPart-object-orbit-sun,
+        result:system-hasPart-sun ;
+    rdfs:label "SolarSystem" .
+
+result:direct a owl:ObjectProperty ;
+    rdfs:label "direct" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:gravitation-bind-system a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:bind ;
+            owl:someValuesFrom result:system ],
+        result:gravitation .
+
+result:hasManner a owl:ObjectProperty ;
+    rdfs:label "hasManner" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:not-direct a owl:ObjectProperty ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:object-orbit-sun a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:orbit ;
+            owl:someValuesFrom result:sun ],
+        result:object .
+
+result:object-orbit-hasManner-direct-sun a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:orbit-hasManner-direct ;
+            owl:someValuesFrom result:sun ],
+        result:object-orbit-sun .
+
+result:object-orbit-hasManner-not-direct-sun a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:orbit-hasManner-not-direct ;
+            owl:someValuesFrom result:sun ],
+        result:object-orbit-sun .
+
+result:gravitation a owl:Class ;
+    rdfs:label "gravitation" ;
+    rdfs:subClassOf base:Entity .
+
+result:system-isBindBy-gravitation a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:isBindBy ;
+            owl:someValuesFrom result:gravitation ],
+        result:system .
+
+result:system-hasPart-object a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:hasPart ;
+            owl:someValuesFrom result:object ],
+        result:system .
+
+result:system-hasPart-object-orbit-sun a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:hasPart ;
+            owl:someValuesFrom result:object-orbit-sun ],
+        result:system-hasPart-object .
+
+result:system-hasPart-sun a owl:Class ;
+    rdfs:subClassOf [ a owl:Restriction ;
+            owl:onProperty result:hasPart ;
+            owl:someValuesFrom result:sun ],
+        result:system .
+
+result:bind a owl:ObjectProperty ;
+    rdfs:label "bind" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:isBindBy owl:inverseOf result:bind ;
+    rdfs:label "isBindBy" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:orbit a owl:ObjectProperty ;
+    rdfs:label "orbit" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:orbit-hasManner-direct a owl:ObjectProperty ;
+    rdfs:subPropertyOf result:orbit .
+
+result:orbit-hasManner-not-direct a owl:ObjectProperty ;
+    rdfs:subPropertyOf result:orbit .
+
+result:hasPart a owl:ObjectProperty ;
+    rdfs:label "hasPart" ;
+    rdfs:subPropertyOf base:Out_ObjectProperty .
+
+result:object a owl:Class ;
+    rdfs:label "object" ;
+    rdfs:subClassOf base:Entity .
+
+result:system a owl:Class ;
+    rdfs:label "system" ;
+    rdfs:subClassOf base:Entity.
+
+result:sun a owl:Class ;
+    rdfs:label "sun" ;
+    rdfs:subClassOf base:Entity .
+

examples/example.py

-#!/usr/bin/python3.10
-# -*-coding:Utf-8 -*
-
-#==============================================================================
-# ontoScorer: [brief description of the module]
-#------------------------------------------------------------------------------
-# Detailed module description, if needed
-#==============================================================================
-
-# TODO

requirements.txt

 rdflib
+scikit-learn