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dice-group / owlapy

OWLAPY is a Python Framework for creating and manipulating OWL Ontologies.
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OWLAPY

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OWLAPY

OWLAPY is a Python Framework for creating and manipulating OWL Ontologies.

Have a look at the Documentation.

Installation

Installation from Source

git clone https://github.com/dice-group/owlapy
conda create -n temp_owlapy python=3.10.13 --no-default-packages && conda activate temp_owlapy && pip3 install -e .

or

pip3 install owlapy
# To download RDF knowledge graphs
wget https://files.dice-research.org/projects/Ontolearn/KGs.zip -O ./KGs.zip && unzip KGs.zip
pytest -p no:warnings -x # Running  147 tests ~ 35 secs

Examples

OWL Reasoning from Command line

Click me! ```shell owlapy --path_ontology "KGs/Family/family-benchmark_rich_background.owl" --inference_types "all" --out_ontology "enriched_family.owl" ``` ```--inference_types``` can be specified by selecting one from ``` ["InferredClassAssertionAxiomGenerator", "InferredSubClassAxiomGenerator", "InferredDisjointClassesAxiomGenerator", "InferredEquivalentClassAxiomGenerator", "InferredEquivalentDataPropertiesAxiomGenerator", "InferredEquivalentObjectPropertyAxiomGenerator", "InferredInverseObjectPropertiesAxiomGenerator", "InferredSubDataPropertyAxiomGenerator", "InferredSubObjectPropertyAxiomGenerator", "InferredDataPropertyCharacteristicAxiomGenerator", "InferredObjectPropertyCharacteristicAxiomGenerator"] ```

Exploring OWL Ontology

Click me! ```python from owlapy.owl_ontology_manager import SyncOntologyManager ontology_path = "KGs/Family/father.owl" onto = SyncOntologyManager().load_ontology(ontology_path) print({owl_class.reminder for owl_class in onto.classes_in_signature()}) # {'Thing', 'female', 'male', 'person'} print({individual.reminder for individual in onto.individuals_in_signature()}) # {'michelle', 'stefan', 'martin', 'anna', 'heinz', 'markus'} print({object_property.reminder for object_property in onto.object_properties_in_signature()}) # {'hasChild'} for owl_subclass_of_axiom in onto.get_tbox_axioms(): print(owl_subclass_of_axiom) # OWLEquivalentClassesAxiom([OWLClass(IRI('http://example.com/father#', 'male')), OWLObjectComplementOf(OWLClass(IRI('http://example.com/father#', 'female')))],[]) # OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'female')),super_class=OWLClass(IRI('http://example.com/father#', 'person')),annotations=[]) # OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'male')),super_class=OWLClass(IRI('http://example.com/father#', 'person')),annotations=[]) # OWLSubClassOfAxiom(sub_class=OWLClass(IRI('http://example.com/father#', 'person')),super_class=OWLClass(IRI('http://www.w3.org/2002/07/owl#', 'Thing')),annotations=[]) # OWLObjectPropertyRangeAxiom(OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),OWLClass(IRI('http://example.com/father#', 'person')),[]) # OWLObjectPropertyDomainAxiom(OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),OWLClass(IRI('http://example.com/father#', 'person')),[]) for axiom in onto.get_abox_axioms(): print(axiom) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),class_expression=OWLClass(IRI('http://example.com/father#', 'female')),annotations=[]) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'michelle')),class_expression=OWLClass(IRI('http://example.com/father#', 'female')),annotations=[]) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'martin')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[]) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[]) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[]) # OWLClassAssertionAxiom(individual=OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')),class_expression=OWLClass(IRI('http://example.com/father#', 'male')),annotations=[]) # OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),annotations=[]) # OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'martin')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),annotations=[]) # OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'stefan')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'markus')),annotations=[]) # OWLObjectPropertyAssertionAxiom(subject=OWLNamedIndividual(IRI('http://example.com/father#', 'anna')),property_=OWLObjectProperty(IRI('http://example.com/father#', 'hasChild')),object_=OWLNamedIndividual(IRI('http://example.com/father#', 'heinz')),annotations=[]) ```

OWL Knowledge Engineering

Click me! ```python from owlapy.class_expression import OWLClass, OWLObjectIntersectionOf, OWLObjectSomeValuesFrom from owlapy.owl_property import OWLObjectProperty from owlapy import owl_expression_to_sparql, owl_expression_to_dl from owlapy.owl_ontology_manager import OntologyManager from owlapy.owl_axiom import OWLDeclarationAxiom, OWLClassAssertionAxiom from owlapy.owl_individual import OWLNamedIndividual, IRI from owlapy.static_funcs import create_ontology # Using owl classes to create a complex class expression male = OWLClass("http://example.com/society#male") hasChild = OWLObjectProperty("http://example.com/society#hasChild") hasChild_male = OWLObjectSomeValuesFrom(hasChild, male) teacher = OWLClass("http://example.com/society#teacher") teacher_that_hasChild_male = OWLObjectIntersectionOf([hasChild_male, teacher]) # You can render and print owl class expressions in Description Logics syntax or convert it to SPARQL for example. print(owl_expression_to_dl(teacher_that_hasChild_male)) # (∃ hasChild.male) ⊓ teacher print(owl_expression_to_sparql(teacher_that_hasChild_male)) # SELECT DISTINCT ?x WHERE { ?x ?s_1 . ?s_1 a . ?x a . } } # Create an ontology via ontology manager directly ontology = create_ontology("file:/example_ontology.owl",with_owlapi=False) john = OWLNamedIndividual("http://example.com/society#john") male_declaration_axiom = OWLDeclarationAxiom(male) hasChild_declaration_axiom = OWLDeclarationAxiom(hasChild) john_declaration_axiom = OWLDeclarationAxiom(john) john_a_male_assertion_axiom = OWLClassAssertionAxiom(john, male) ontology.add_axiom([male_declaration_axiom, hasChild_declaration_axiom, john_declaration_axiom, john_a_male_assertion_axiom]) ontology.save(inplace=True) ``` Every OWL object that can be used to classify individuals, is considered a class expression and inherits from [OWLClassExpression](https://dice-group.github.io/owlapy/autoapi/owlapy/class_expression/class_expression/index.html#owlapy.class_expression.class_expression.OWLClassExpression) class. In the above examples we have introduced 3 types of class expressions: - [OWLClass](https://dice-group.github.io/owlapy/autoapi/owlapy/class_expression/owl_class/index.html#owlapy.class_expression.owl_class.OWLClass), - [OWLObjectSomeValuesFrom](https://dice-group.github.io/owlapy/autoapi/owlapy/class_expression/restriction/index.html#owlapy.class_expression.restriction.OWLObjectSomeValuesFrom) - [OWLObjectIntersectionOf](https://dice-group.github.io/owlapy/autoapi/owlapy/class_expression/nary_boolean_expression/index.html#owlapy.class_expression.nary_boolean_expression.OWLObjectIntersectionOf). Like we showed in this example, you can create all kinds of class expressions using the OWL objects in [owlapy api](https://dice-group.github.io/owlapy/autoapi/owlapy/index.html).

Logical Inference

Click me! ```python from owlapy.owl_ontology_manager import OntologyManager from owlapy.owl_reasoner import SyncReasoner from owlapy.static_funcs import stopJVM ontology_path = "KGs/Family/family-benchmark_rich_background.owl" # Available OWL Reasoners: 'HermiT', 'Pellet', 'JFact', 'Openllet' sync_reasoner = SyncReasoner(ontology = ontology_path, reasoner="Pellet") onto = OntologyManager().load_ontology(ontology_path) # Iterate over defined owl Classes in the signature for i in onto.classes_in_signature(): # Performing type inference with Pellet instances=sync_reasoner.instances(i,direct=False) print(f"Class:{i}\t Num instances:{len(instances)}") stopJVM() ```

Ontology Enrichment

Click me! An Ontology can be enriched by inferring many different axioms. ```python from owlapy.owl_reasoner import SyncReasoner from owlapy.static_funcs import stopJVM sync_reasoner = SyncReasoner(ontology="KGs/Family/family-benchmark_rich_background.owl", reasoner="Pellet") # Infer missing class assertions sync_reasoner.infer_axioms_and_save(output_path="KGs/Family/inferred_family-benchmark_rich_background.ttl", output_format="ttl", inference_types=[ "InferredClassAssertionAxiomGenerator", "InferredEquivalentClassAxiomGenerator", "InferredDisjointClassesAxiomGenerator", "InferredSubClassAxiomGenerator", "InferredInverseObjectPropertiesAxiomGenerator", "InferredEquivalentClassAxiomGenerator"]) stopJVM() ```

Check also the examples and tests folders.

Sklearn to OWL Ontology

Click me! ```python from owlapy.owl_ontology_manager import SyncOntologyManager from owlapy.util_owl_static_funcs import csv_to_rdf_kg import pandas as pd from sklearn.datasets import load_iris data = load_iris() df = pd.DataFrame(data.data, columns=data.feature_names) df.to_csv("iris_dataset.csv", index=False) path_kg = "iris_kg.owl" # Construct an RDF Knowledge Graph from a CSV file csv_to_rdf_kg(path_csv="iris_dataset.csv", path_kg=path_kg, namespace="http://owlapy.com/iris") onto = SyncOntologyManager().load_ontology(path_kg) assert len(onto.get_abox_axioms()) == 750 ```

How to cite

Currently, we are working on our manuscript describing our framework.