jcel

jcel is a reasoner for the description logic EL+. It uses the OWL API and can be used as a plug-in for Protege.

Download

<dependency>
  <groupId>de.tu-dresden.inf.lat.jcel</groupId>
  <artifactId>jcel-owlapi</artifactId>
  <version>0.24.1</version>
</dependency>

Author

Julian Alfredo Mendez

Licenses

Apache 2.0, LGPL 3.0

Main features

is an OWL 2 EL reasoner (albeit currently with some limitations)
uses the OWL API
can be used in Protégé
is free software and is licensed under Apache License, Version 2.0 and GNU Lesser General Public License version 3
is fully implemented in Java
evaluated by the SEALS Community having the lowest Average Reasoning Time in 2010

Suggested technologies

Java Development Kit 11 (or higher)
Apache Maven 3.6.3 (or higher)

Source code

The project is hosted on GitHub. To check out and compile the project with Apache Maven:

$ git clone https://github.com/julianmendez/jcel.git
$ cd jcel
$ mvn clean install

The library, its sources and its Javadoc will be in jcel-library/target, the plug-in will be in jcel-plugin/target, the standalone will be in jcel-standalone/target, and the release ZIP file will be in target.

To compile the project offline, first download the dependencies:

$ mvn dependency:go-offline

and once offline, use:

$ mvn --offline clean install

The bundles uploaded to Sonatype are created with:

$ mvn clean install -DperformRelease=true

and then on each module:

$ cd target
$ jar -cf bundle.jar jcel-*

and on the main directory:

$ cd target
$ jar -cf bundle.jar jcel-parent-*

The version number is updated with:

$ mvn versions:set -DnewVersion=NEW_VERSION

where NEW_VERSION is the new version. The file VersionInfo.java is updated manually.

Architecture

Modules

The version under development has the following modules:

jcel-coreontology : set of normalized axioms
jcel-core : classification algorithms using only normalized axioms
jcel-ontology : set of all possible axioms and a procedure to normalize them
jcel-reasoner : reasoner that can classify an ontology and can compute entailment
jcel-owlapi : OWL API interface, performs the translation between the OWL API axioms and jcel axioms
jcel-protege : module to connect to Protégé

It also has the following module used to build the release:

jcel-library : module to create the library, its sources and its javadoc
jcel-plugin : module to create the jar for Protégé
jcel-standalone : module to create the standalone application
jcel-distribution : module to create the release, a single ZIP file

Algorithm

translate OWL API axioms into jcel axioms, which are composed by integer numbers
detect the expressivity used in the axioms
apply normalization rules to the set of axioms, producing a set of normalized axioms and auxiliary entities if necessary
saturate the set of normalized axioms with deduced object property axioms
create an extended ontology based on the set of normalized axioms
apply the completion rules while there is some change in the affected sets
remove the auxiliary entities
build a graph containing direct subsumers (parents), direct subsumees (children) and equivalents
create OWL API data structures based on the jcel’s integer representation

Package dependencies

If we consider each package as a node, and each dependency between two packages as a directed edge, the structure of package dependency should be a directed acyclic graph (DAG). The packages should only make public those classes that are or could be used by another package preserving the DAG structure.

Example

This file is an example of how to start jcel.

This file is an example ontology using ELHIfR+.

Ontologies:

Gene Ontology: input owl krss, output xml
NCI Thesaurus: input owl, output xml
CEL GALEN: input owl krss, output xml
Not GALEN: input owl, output xml
Foundational Model of Anatomy
SNOMED CT

Release notes

See release notes.

Older versions

More information

Frequently Asked Questions

References

Support

Any bug or unexpected behavior can be directly reported by sending a message to the author. Questions and suggestions are also very welcome. In case you need more information, please contact julianmendez.

News

@jcelreasoner