julianmendez / jcel

Reasoner for the description logic EL+.

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

• all-in-one ZIP file
• The Central Repository
• all releases
• as dependency:

<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

• Git SHA
• old SVN revision
• releases

More information

• Frequently Asked Questions

References

• Theoretical foundation:
  • Master's thesis by J. A. Mendez
  • Master's thesis by Q. H. Vu
  • Ph.D. thesis by B. Suntisrivaraporn
• CEL: main page - source code
• OWL API: main page
• OWL 2: OWL Working Group

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

jcel's Issues

Some dead links on the JCEL Homepage (http://julianmendez.github.io/jcel/)

The homepage of JCEL currently has some links that don't lead to the right places.

In the "Example" section, there are some links to OWL and KRSS file downloads, which are redirected to https://tu-dresden.de/ing/informatik/thi/lat/forschung/software - Clicking on JCEL there leads to http://julianmendez.github.io/jcel/ again.

TranslationException error when normalizing ontology.

Hello. I have tried to normalize the ontology found here but I get this error:

de.tudresden.inf.lat.jcel.owlapi.translator.TranslationException: de.tudresden.inf.lat.jcel.owlapi.translator.TranslationException: Object cannot be translated: 'ObjectUnionOf(<http://purl.obolibrary.org/obo/UBERON_0001299> <http://purl.obolibrary.org/obo/UBERON_0006653>)'.

I also have a modified version of the previous ontology that can be downloaded from here. In this case I get this error:

de.tudresden.inf.lat.jcel.owlapi.translator.de.tudresden.inf.lat.jcel.owlapi.translator.TranslationException: de.tudresden.inf.lat.jcel.owlapi.translator.TranslationException: The translation map is incomplete. Item id was not found: 'https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships'

This is. my code:

from de.tudresden.inf.lat.jcel.owlapi.main import JcelReasoner
from org.semanticweb.owlapi.apibinding import OWLManager

ont_manager = OWLManager.createOWLOntologyManager()
ontology = ont_manager.loadOntologyFromOntologyDocument(java.io.File("ontology_path"))
jreasoner = JcelReasoner(ontology, False)

The code is written in Python but I am using JPype to interface with Java.
Would you please help me to figure out what is happening?

jcel version (0.25?)

the latest jcel version was released in 2016.
If possible, release a new version so that it is automatically imported into the latest version of protege