owlapi-lite

OWLAPI-Lite

DOI contributions welcome Maven Central

OWLAPI-Lite is a light-weight wrapper for the OWLAPI that enables faster development of OWL ontologies with more concise code using the power of the Manchester OWL Syntax and related parsers. The wrapper does not make use of all the features of the more powerful OWLAPI. Rather, it is designed specifically for rapid and concise ontology construction in workflows involving semantic data engineering. It can also be used in contexts such as educational and demonstration settings in courses, workshops and tutorials. In particular, the library can also be used in Jupyter notebooks using a Java kernel such as the IJava kernel.

Usage in Jupyter notebooks

Requirements
  1. Jupyter notebooks
  2. IJava Jupyter kernel
  3. Java JDK 21+ linked to your IJava kernel
Importing

When using OWLAPI-Lite with Jupyter notebooks using the IJava kernel, the recommended way to import the library is to use %maven Magics in the following way (the command should be in its own dedicated cell):

%maven io.github.kodymoodley:owlapi-lite:1.2.0

If that does not work, you could try %%loadFromPOM:

%%loadFromPOM
<dependency>
    <groupId>io.github.kodymoodley</groupId>
    <artifactId>owlapi-lite</artifactId>
    <version>1.2.0</version>
</dependency>

The latter method is known to potentially cause problems due to .ivy2 caching conflicts. If you encounter this issue, the last resort is to download the .jar file of OWLAPI-Lite with packaged dependencies from the releases section and import this file manually into your IJava notebook by running the following command from a single dedicated cell in the notebook:

%jars path/to/jar/file/owlapi-lite-${version}.jar

Another known issue is when using OWLAPI-Lite from mybinder is the following error:

java.lang.NullPointerException: Cannot invoke "org.semanticweb.owlapi.model.OWLStorerFactory.createStorer()" because "storerFactory" is null at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1370) at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1349) at io.github.kodymoodley.owlapilite.OWLAPILiteFactory.saveOntology(OWLAPILiteFactory.java:1530) at .(#93:2)

If you encounter this error, make use of the %jars method above to import OWLAPI-Lite in your Jupyter notebook.

Dependencies

The OWLAPI-Lite release for Jupyter notebooks is bundled into one .jar file for convenience. This file includes the following dependencies (see pom.xml for specific versions):

  1. The OWL API released under both the GNU Lesser General Public License (LGPL) and the Apache 2.0 License.
  2. The HermiT OWL reasoner released under the GNU Lesser General Public License (LGPL).
  3. The JFact OWL reasoner released under the GNU Lesser General Public License (LGPL).
  4. The ELK OWL reasoner released under the Apache 2.0 License.
  5. The owlexplanation library released under the GNU Lesser General Public License (LGPL).

Usage in Maven projects

Include the following dependency in your pom.xml

<dependency>
	<groupId>io.github.kodymoodley</groupId>
	<artifactId>owlapi-lite</artifactId>
	<version>1.2.0</version>
</dependency>

Examples and documentation

For more information on how to use OWLAPI-Lite, see the Javadocs and examples below.

Examples: ontology editing
import io.github.kodymoodley.owlapilite.*;
import org.semanticweb.owlapi.model.*;

// create a new OWLAPILiteFactory instance which allows the construction and manipulation of OWL ontologies (default OWL reasoner is JFACT)
OWLAPILiteFactory s = new OWLAPILiteFactory(); 
// create a new OWL ontology by specifying an IRI string and set it to the currently selected (active) ontology
s.createOntology("http://com.kodymoodley/ontologies/2020/testontology#");
// create multiple class names (each separated by a space) and add them to the currently selected ontology
s.createClasses("Penguin Peacock Bird Robin FlyingOrganism Fish Wing Gender Person Female Male");

// change namespace of the editor (temporarily) so we can add or reuse terms from external ontologies or vocabularies
s.setNamespace("http://schema.org/");
// add an object property to the same ontology which will now have the IRI <http://schema.org/parent> (reusing the term from Schema.org)
s.createObjectProperty("parent");

// create multiple object properties (each separated by a space) and add them to the currently selected ontology
s.createObjectProperties("hasPart isPartOf hasGender knows eats hunts");
// create multiple named individuals (each separated by a space) and add them to the currently selected ontology
s.createIndividuals("tweety woody nemo sharky sheila feather1");
// create multiple data properties (each separated by a space) and add them to the currently selected ontology
s.createDataProperties("hasWeight name bornOn"); 

// make an object property transitive
s.makeTransitive("eats"); 
// make an object property symmetric
s.makeSymmetric("knows"); 
// make an object property irreflexive
s.makeIRReflexive("hasGender"); 
// make an object property asymmetric
s.makeAntiSymmetric("hasGender"); 
		
// set whether to render OWL entities (classes, individuals, properties, axioms etc.) using full IRIs or shortform label
s.setFullIRIRendering(true); 

// create an OWL data property assertion axiom and add it to the currently selected ontology
s.createAxiom("tweety Type: hasWeight value \"300.56\"^^xsd:double");
// create an OWL class assertion axiom and add it to the currently selected ontology
s.createAxiom("tweety Type: hasGender exactly 1 Gender"); 
s.createAxiom("tweety Type: Penguin");
// create an OWL object property assertion axiom and add it to the currently selected ontology
s.createObjectPropertyAssertion("woody knows nemo"); 

// create OWL subPropertyOf axiom and add it to the currently selected ontology
s.createAxiom("eats subPropertyOf: hunts"); 
// create inverse object property axiom and add it to the currently selected ontology
s.createAxiom("isPartOf inverseOf: hasPart"); 
// create object property domain axiom and add it to the currently selected ontology
s.createAxiom("knows Domain: Person"); 
// create object property range axiom and add it to the currently selected ontology
s.createAxiom("knows Range: Person"); 

// create OWL subClassOf axiom and add it to the currently selected ontology
s.createAxiom("Penguin subClassOf eats some Fish"); 
s.createAxiom("Penguin subClassOf Bird");
s.createAxiom("Bird subClassOf FlyingOrganism");
s.createAxiom("Penguin subClassOf not FlyingOrganism");
// create OWL equivalent classes axiom and add it to the currently selected ontology
s.createAxiom("Gender equivalentTo: Male or Female"); 
// create OWL equivalent classes axiom and add it to the currently selected ontology
s.createAxiom("Male disjointWith: Female"); 
// create an OWL subClassOf axiom using nominals and add it to the currently selected ontology
s.createAxiom("{tweety,woody} subClassOf Bird"); 

s.createOntology("http://com.kodymoodley/ontologies/2020/testontology2#");
// set or switch the "active" ontology by specifying the IRI of the ontology to switch to
s.setOntology("http://com.kodymoodley/ontologies/2020/testontology2#");
// prints to console the IRI of the currently selected ontology
s.getOntology(); 
// prints to console the IRIs of all ontologies created / loaded within the current context (instance of the OWLAPILiteFactory)
s.getOntologies(); 
// prints to console a structured representation of the main OWL entities in the active ontology
s.printOntology();
// prints active ontology metrics (e.g. number of classes, axioms of a certain type etc.)
s.printOntologyStats(); 

// save active ontology to local file using Manchester OWL syntax
s.saveOntology("testontology.owl"); 
// load an ontology into this context from a remote URL
s.loadFromURL("https://protege.stanford.edu/ontologies/pizza/pizza.owl"); 
// load an ontology into this context from a local file path. WARNING: you cannot load multiple ontologies with the same IRI into the same context!
s.loadFromFile("path/to/ontology.owl");	
// remove selected ontology from current context (OWLAPILiteFactory instance) 
s.removeOntology(); 
// remove ontology with specified IRI from current context (OWLAPILiteFactory instance) 
s.removeOntology("http://com.kodymoodley/ontologies/2020/testontology2#"); 

// remove all axioms from the currently selected ontology
s.resetOntology(); 
// remove multiple class names from currently selected ontology
s.removeClasses("Bird Penguin"); 
// remove multiple object properties from currently selected ontology
s.removeObjectProperties("knows hasPart"); 
// remove multiple data properties from currently selected ontology
s.removeDataProperties("hasWeight name"); 
// remove multiple individual names from currently selected ontology
s.removeIndividuals("tweety woody"); 
// remove an axiom from the currently selected ontology
s.removeAxiom("Penguin subClassOf eats some Fish");
Examples: reasoning
OWLAPILiteFactory s = new OWLAPILiteFactory();

...

// Switch or set OWL reasoner 
s.setOWLReasoner(SelectedReasoner.HERMIT); 

// prints to console Yes if currently selected ontology is consistent, No otherwise
s.owlReasoner.isConsistent(); 
// computes and prints to console all explanations for the inconsistency of the selected ontology (provided it is inconsistent)
s.owlReasoner.explainInconsistency(); 

// prints to console Yes if the given class expression is satisfiable, No otherwiseNo otherwise
s.owlReasoner.isSatisfiable("Penguin");
// computes and prints to console all explanations for the unsatisfiability of the given class expression w.r.t. the active ontology (provided it is indeed unsatisfiable)
s.owlReasoner.explainUnsatisfiability("Penguin"); 

// prints to console Yes if the given axiom is entailed by the currently selected ontology, No otherwise
s.owlReasoner.isEntailed("Robin subClassOf FlyingOrganism"); 
// computes and prints to console all explanations for the entailment of the given axiom w.r.t. the selected ontology (provided it is indeed entailed)
s.owlReasoner.explainEntailment("Robin subClassOf FlyingOrganism"); 

// computes and prints to console all super classes (indirect) for the given class expression
s.owlReasoner.getSuperClasses("Robin");	
// computes and prints to console all sub classes (indirect) for the given class expression
s.owlReasoner.getSubClasses("FlyingOrganism"); 
// computes and prints to console all atomic classes equivalent to the given class expression
s.owlReasoner.getEquivalentClasses("Robin and not FlyingOrganism");

// computes and prints to console all class names for which the given individual is an instance
s.owlReasoner.getTypes("tweety"); 
// for each individual name in the selected ontology, computes and prints to console all class names such that this individual is an instance of the class name
s.owlReasoner.getAllTypes(); 
// computes and prints to console all instances of the given class expression
s.owlReasoner.getInstances("Robin and not FlyingOrganism"); 

// given an object property name R, prints to console all individual name pairs (a,b) such that R(a, b) is an object property assertion entailed by the selected ontology
s.owlReasoner.getObjectPropertyAssertions("knows"); 
// for each object property R in the ontology, prints to console all individual name pairs (a,b) such that R(a, b) is an object property assertion entailed by the active ontology
s.owlReasoner.getAllObjectPropertyAssertions(); 

// prints to console the name of the OWL reasoner which is currently being used by the OWLAPILiteFactory instance
s.owlReasoner.getName(); 
// prints to console the name of the OWL 2 profile which the selected OWL reasoner supports
s.owlReasoner.getOWLProfile();

For Developers: Building the library from source

Requirements:
Steps:

  1. Get a copy of the code:

     git clone https://github.com/kodymoodley/owlapi-lite.git

  2. Change into the owlapi-lite/ directory.

  3. Type mvn clean package. On build completion, the target/ directory will contain two versions of the library: owlapi-lite-${version}.jar and owlapi-lite-${version}-jar-with-dependencies.jar.

License and contributions

The OWLAPI-Lite library is copyrighted by Kody Moodley and released under the GNU Affero License.

Contributions and bug reports are helpful and welcome.

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