From 1b39f6239a7311bdb9938acd2afa243df9047c8c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Aur=C3=A9lien=20Lamercerie?=
<aurelien.lamercerie@tetras-libre.fr>
Date: Fri, 4 Aug 2023 12:50:07 +0200
Subject: [PATCH] Update library and add a main script
---
README.md | 34 +++---
data/generated_ontology.ttl | 104 +++++++++++++++++
data/reference_ontology.ttl | 109 ++++++++++++++++++
main.py | 30 +++++
ontoScorer/__init__.py | 15 +--
.../__pycache__/__init__.cpython-311.pyc | Bin 0 -> 607 bytes
.../__pycache__/metrics.cpython-311.pyc | Bin 0 -> 1704 bytes
.../__pycache__/ontology.cpython-311.pyc | Bin 0 -> 1930 bytes
ontoScorer/__pycache__/report.cpython-311.pyc | Bin 0 -> 2283 bytes
ontoScorer/__pycache__/scorer.cpython-311.pyc | Bin 0 -> 1726 bytes
ontoScorer/metrics.py | 20 +++-
ontoScorer/ontology.py | 27 ++++-
ontoScorer/report.py | 34 +++++-
ontoScorer/scorer.py | 26 ++++-
tests/__init__.py | 10 --
15 files changed, 367 insertions(+), 42 deletions(-)
create mode 100644 data/generated_ontology.ttl
create mode 100644 data/reference_ontology.ttl
create mode 100644 main.py
create mode 100644 ontoScorer/__pycache__/__init__.cpython-311.pyc
create mode 100644 ontoScorer/__pycache__/metrics.cpython-311.pyc
create mode 100644 ontoScorer/__pycache__/ontology.cpython-311.pyc
create mode 100644 ontoScorer/__pycache__/report.cpython-311.pyc
create mode 100644 ontoScorer/__pycache__/scorer.cpython-311.pyc
diff --git a/README.md b/README.md
index d295f3e..8e95455 100644
--- a/README.md
+++ b/README.md
@@ -21,27 +21,27 @@ All dependencies are listed in **requirements.txt**.
We recommend creating a virtual environment before proceeding:
-1. Create a virtual environment:
-> python3 -m venv env
+1. Create a virtual environment: `python3 -m venv env`
-2. Activate the virtual environment:
-> source env/bin/activate
+2. Activate the virtual environment: `source env/bin/activate`
## Usage
Here's an example of how to use ontoScorer:
-> from ontoScorer import OntoScorer
->
-> # Initialize the scorer
-> scorer = OntoScorer("path/to/reference_ontology.ttl", "path/to/generated_ontology.ttl")
->
-> # Compare the ontologies
-> scorer.compare()
->
-> # Print the scores
-> scorer.print_scores()
->
-> # Generate a report
-> scorer.generate_report("path/to/report.txt")
+```python
+from ontoScorer import OntoScorer
+
+# Initialize the scorer
+scorer = OntoScorer("path/to/reference_ontology.ttl", "path/to/generated_ontology.ttl")
+
+# Compare the ontologies
+scorer.compare()
+
+# Print the scores
+scorer.print_scores()
+
+# Generate a report
+scorer.generate_report("path/to/report.txt")
+```
diff --git a/data/generated_ontology.ttl b/data/generated_ontology.ttl
new file mode 100644
index 0000000..2b5ee47
--- /dev/null
+++ b/data/generated_ontology.ttl
@@ -0,0 +1,104 @@
+@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" .
+
diff --git a/data/reference_ontology.ttl b/data/reference_ontology.ttl
new file mode 100644
index 0000000..2b97132
--- /dev/null
+++ b/data/reference_ontology.ttl
@@ -0,0 +1,109 @@
+@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 .
+
diff --git a/main.py b/main.py
new file mode 100644
index 0000000..fe59030
--- /dev/null
+++ b/main.py
@@ -0,0 +1,30 @@
+#!/usr/bin/python3.10
+# -*-coding:Utf-8 -*
+
+#==============================================================================
+# ontoScorer: [brief description of the module]
+#------------------------------------------------------------------------------
+# Detailed module description, if needed
+#==============================================================================
+
+from ontoScorer.scorer import OntoScorer
+
+def main():
+ # 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"
+
+ # Initialize the scorer
+ scorer = OntoScorer(REFERENCE_ONTOLOGY_PATH, GENERATED_ONTOLOGY_PATH)
+
+ # Compare the ontologies
+ scorer.compare()
+
+ # Generate a report
+ scorer.generate_report()
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff --git a/ontoScorer/__init__.py b/ontoScorer/__init__.py
index 4415d78..162f653 100644
--- a/ontoScorer/__init__.py
+++ b/ontoScorer/__init__.py
@@ -1,10 +1,5 @@
-#!/usr/bin/python3.10
-# -*-coding:Utf-8 -*
-
-#==============================================================================
-# ontoScorer: [brief description of the module]
-#------------------------------------------------------------------------------
-# Detailed module description, if needed
-#==============================================================================
-
-# TODO
+# -- Update System Path
+import os, sys
+LIB_PATH = os.path.dirname(os.path.abspath(__file__)) + '/'
+os.chdir(LIB_PATH)
+sys.path.insert(0, os.path.abspath(LIB_PATH))
diff --git a/ontoScorer/__pycache__/__init__.cpython-311.pyc b/ontoScorer/__pycache__/__init__.cpython-311.pyc
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diff --git a/ontoScorer/metrics.py b/ontoScorer/metrics.py
index 4415d78..e905353 100644
--- a/ontoScorer/metrics.py
+++ b/ontoScorer/metrics.py
@@ -4,7 +4,23 @@
#==============================================================================
# ontoScorer: [brief description of the module]
#------------------------------------------------------------------------------
-# Detailed module description, if needed
+# Detailed module description
#==============================================================================
-# TODO
+from sklearn.metrics import precision_score, recall_score, f1_score
+
+class Metrics:
+ def __init__(self):
+ self.precision = 0
+ self.recall = 0
+ self.f1 = 0
+
+ def calculate(self, 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]
+
+ self.precision = precision_score(y_true, y_pred)
+ self.recall = recall_score(y_true, y_pred)
+ self.f1 = f1_score(y_true, y_pred)
+
diff --git a/ontoScorer/ontology.py b/ontoScorer/ontology.py
index 4415d78..f9403cb 100644
--- a/ontoScorer/ontology.py
+++ b/ontoScorer/ontology.py
@@ -7,4 +7,29 @@
# Detailed module description, if needed
#==============================================================================
-# TODO
+from rdflib import Graph, OWL
+from rdflib.namespace import split_uri
+
+class Ontology:
+ def __init__(self, ontology_path):
+ self.path = ontology_path
+ self.graph = self.load_ontology(ontology_path)
+ self.classes = self.get_classes()
+
+ def load_ontology(self, path):
+ g = Graph()
+ g.parse(path, format="ttl")
+ return g
+
+ def get_classes(self):
+ classes = set()
+ triplets_count = 0
+ for s, p, o in self.graph.triples((None, None, None)):
+ triplets_count += 1
+ if o == OWL.Class:
+ _, class_name = split_uri(s)
+ classes.add(class_name)
+ return classes
+
+ def compare_to(self, other_ontology):
+ return self.classes, other_ontology.classes
\ No newline at end of file
diff --git a/ontoScorer/report.py b/ontoScorer/report.py
index 4415d78..30f7659 100644
--- a/ontoScorer/report.py
+++ b/ontoScorer/report.py
@@ -7,4 +7,36 @@
# Detailed module description, if needed
#==============================================================================
-# TODO
+class Report:
+ def __init__(self, reference_ontology, generated_ontology, comparison_result, metrics):
+ self.reference_ontology = reference_ontology
+ self.generated_ontology = generated_ontology
+ self.comparison_result = comparison_result
+ self.metrics = metrics
+
+ def generate(self):
+ report_str = "=== Ontology Evaluation Report ===\n"
+
+ report_str += f"\nReference Ontology: {self.reference_ontology.path}"
+ report_str += f"\nNumber of classes in Reference Ontology: {len(self.reference_ontology.classes)}"
+
+ report_str += f"\n\nGenerated Ontology: {self.generated_ontology.path}"
+ report_str += f"\nNumber of classes in Generated Ontology: {len(self.generated_ontology.classes)}"
+
+ # Comparison of the number of classes
+ report_str += "\n\nComparison Result: "
+ if len(self.reference_ontology.classes) > len(self.generated_ontology.classes):
+ report_str += "The generated ontology has fewer classes than the reference ontology."
+ elif len(self.reference_ontology.classes) < len(self.generated_ontology.classes):
+ report_str += "The generated ontology has more classes than the reference ontology."
+ else:
+ report_str += "The generated ontology and the reference ontology have the same number of classes."
+
+ report_str += "\n\nEvaluation Metrics:"
+ report_str += f"\nPrecision: {self.metrics.precision}"
+ report_str += f"\nRecall: {self.metrics.recall}"
+ report_str += f"\nF1 Score: {self.metrics.f1}"
+
+ return report_str
+
+
diff --git a/ontoScorer/scorer.py b/ontoScorer/scorer.py
index 4415d78..2ed8085 100644
--- a/ontoScorer/scorer.py
+++ b/ontoScorer/scorer.py
@@ -7,4 +7,28 @@
# Detailed module description, if needed
#==============================================================================
-# TODO
+from ontology import Ontology
+from report import Report
+from metrics import Metrics
+
+class OntoScorer:
+ def __init__(self, reference_ontology_path, generated_ontology_path):
+ self.reference_ontology = Ontology(reference_ontology_path)
+ self.generated_ontology = Ontology(generated_ontology_path)
+ self.metrics = Metrics()
+
+ def compare(self):
+ self.comparison_result = self.reference_ontology.compare_to(self.generated_ontology)
+ self.metrics.calculate(*self.comparison_result)
+
+ def generate_report(self):
+ report = Report(self.reference_ontology,
+ self.generated_ontology,
+ self.comparison_result,
+ self.metrics)
+ print(report.generate())
+
+
+ # def generate_report(self, report_path):
+ # report = Report(self.comparison_result, self.metrics)
+ # report.generate(report_path)
diff --git a/tests/__init__.py b/tests/__init__.py
index 4415d78..e69de29 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -1,10 +0,0 @@
-#!/usr/bin/python3.10
-# -*-coding:Utf-8 -*
-
-#==============================================================================
-# ontoScorer: [brief description of the module]
-#------------------------------------------------------------------------------
-# Detailed module description, if needed
-#==============================================================================
-
-# TODO
--
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