kbss-cvut / jopa

Java OWL Persistence API

JOPA - Java OWL Persistence API

JOPA is a Java OWL persistence framework aimed at efficient programmatic access to OWL2 ontologies and RDF graphs in Java. The system is based on integrity constraints [1] in OWL that JOPA uses to establish a contract between a JOPA-enabled Java application and an OWL ontology. Note, however, that for practical purposes of working with triple stores, this OWL integrity constraints-based contract is not required.

The library architecture and API is similar to JPA (see [2]) so that Java developers find it familiar.

Main Features

• Object-ontological mapping (OOM) based on integrity constraints
• Explicit access to inferred knowledge
• Access to unmapped properties and individual's types
• Transactions
• Separate storage access layer - Jena, OWLAPI, RDF4J drivers are available

Object-ontological Mapping Based on Integrity Constraints

Similarly to object-relational mapping (ORM), OOM enables to map ontological constructs to constructs of an object-oriented programming language and vice versa.

More specifically, OOM in JOPA maps (using the JLS [3] terminology):

Ontology	OO Language
OWL Class	Reference type
Object property	Reference type member
Data property	Primitive type member (+ String, Date)
Annotation property	Reference or primitive type member
Class assertions	Reference type instance or @Types record

All this means that individuals belonging to an OWL class can be retrieved as instances of a (Java) class.

Note: OOM works also for RDFS ontologies. See the wiki for details.

Here is a simple example of a JOPA entity:

@Namespace(prefix = "skos", namespace="http://www.w3.org/2004/02/skos/core#")
@OWLClass(iri = "skos:Concept")
public class Term {
  @Id
  private URI id;

  @OWLAnnotationProperty(iri = "skos:prefLabel")
  private MultilingualString label;

  @OWLAnnotationProperty(iri = "skos:definition")
  private MultilingualString definition;

  @OWLObjectProperty(iri = "skos:narrower")
  private Set<Term> children;

  @Types
  private Set<String> types;

  @Properties
  private Map<String, Set<String>> properties;
}

Explicit Access to Inferred Knowledge

A member annotated with the @Inferred annotation represents a field whose values are retrieved using a reasoner. As such, they can, for example, contain values of an inverse object property (like in the Jedi example).

There are limitations to this: JOPA requires explicit class assertion to be able to load individual as instance of a class. And, inferred values are read-only. These restrictions have pragmatic reasons - if the knowledge is inferred, it cannot be directly modified/removed, so attempting to remove an inferred value does not have any direct effects.

Access to Unmapped Properties and Individual's Types

OOM is not meant to completely capture the ontological model. It would not even make much sense. One of the main features of JOPA is its ability to work with knowledge which is not part of the object model. This is done using members annotated with @Types and @Properties. @Types field contains all OWL classes whose instance the particular individual represented by an object is (except the one mapped by the object's Java class). @Properties field contains values of properties not mapped by object model. This way, the application gets (although limited) access to unmapped property values (e.g. values of newly added properties), without the need to adjust the object model and recompile.

Transactions

JOPA supports object-level transactions. In addition, it makes transactional change visible to the transaction that made them. This means that when you add an instance of some class during a transaction and then list all instances of that class (during the same transaction), you'll see the newly added instance as well.

There are limitations to this approach. Currently, pending changes are not taken into account when doing inference. Also, the current version of RDF4J OntoDriver is not able to include pending changes into results of SPARQL queries.

Separate Storage Access Layer

Similarly to JPA and JDBC driver, JOPA sits on top of an OntoDriver instance, which provides access to the underlying storage. There are two main reasons for such a split - first, it decouples storage-specific API usage from the more generic OOM core. Second, it enables the application to switch the underlying storage with as little as 2-3 lines of configuration code. Nothing else needs to be modified.

Supported storages:

• Jena
• OWLAPI
• RDF4J

Not Supported, yet

JOPA currently does not support referential integrity. This, for example, means that removing an instance that is referenced by another instance is possible even though it should not. Such feature is vital for object-oriented application, but not compatible with the open-world nature of ontologies. Design possibilities and their implications are currently being studied.

Other missing/planned stuff can be found in the GitHub issue tracker and in TODO.md.

Modules

The whole framework consists of several modules:

• JOPA API - definition of the JOPA API, similar to JPA.
• OntoDriver API - API of the storage access layer.
• JOPA implementation - persistence provider implementation.
• OntoDriver RDF4J - OntoDriver implementation for RDF4J-accessed storages.
• OntoDriver OWLAPI - OntoDriver implementation for OWLAPI-accessed files.
• Ontodriver Jena - OntoDriver implementation for Jena-based storages.
• OWL2Java - generates JOPA entities based on integrity constraints in input ontology (see Example01).
• Modelgen - static metamodel generator.
• JOPA Maven plugin - Maven plugin for object model (using OWL2Java) and static metamodel (using Modelgen) generation.

Other modules represent integration tests and various utilities.

Documentation

Check out the Wiki for general information about JOPA, explanation of its features and their usage. The content is being gradually created and updated.

Javadoc of the latest published version is available at https://kbss.felk.cvut.cz/jenkins/job/jopa-stable/javadoc/index.html?overview-summary.html.

For practical examples of JOPA features, see the JOPA examples repository.

Usage

JOPA examples can be found in a separate repository at https://github.com/kbss-cvut/jopa-examples.

A real-world, up-to-date project using JOPA is TermIt - a SKOS-compatible vocabulary manager.

Note that JOPA requires Java 11 or later.

Getting JOPA

There are two ways of getting JOPA for a project:

• Clone repository/download zip and build it with Maven,
• Use a Maven dependency from the Maven central repository.

Basically, the jopa-impl module and one of the OntoDriver implementations is all that is needed:

<dependencies>
    <dependency>
        <groupId>cz.cvut.kbss.jopa</groupId>
        <artifactId>jopa-impl</artifactId>
    </dependency>
    <dependency>
        <groupId>cz.cvut.kbss.jopa</groupId>
        <artifactId>ontodriver-rdf4j</artifactId>
        <!-- OR <artifactId>ontodriver-jena</artifactId> -->
        <!-- OR <artifactId>ontodriver-owlapi</artifactId> -->
    </dependency>
</dependencies>

More Info

More information about JOPA can be found for example in articles [4], [5], [6] and on the GitHub Wiki.

JOPA build status and code metrics can be found at:

• KBSS Jenkins https://kbss.felk.cvut.cz/jenkins,
• KBSS SonarQube https://kbss.felk.cvut.cz/sonarqube.

Performance

A performance comparison of JOPA and other object-triple mapping libraries can be found at https://kbss.felk.cvut.cz/web/otm-benchmark.

A comprehensive comparison - feature and performance - of object-triple mapping libraries is presented in [7].

Related

Some related libraries:

• JB4JSON-LD - Serialization and deserialization of POJOs into JSON-LD. Uses JOPA mapping annotations.
• JOPA-Spring-transaction - Declarative Spring transactions (using the @Transactional annotation) with JOPA.
• Reporting Tool - Real-life use case of JOPA. No longer actively maintained.
• TermIt - A more complex and up-to-date use case of JOPA.

History

Notable changes:

• 1.0.0 - Support for static metamodel generation and mapping multiple inheritance via Java interfaces.
• 0.20.0 - Allow editing inferred attributes (See the wiki for more details). Support IN, NOT LIKE, <> operators in SOQL.
• 0.19.0 - Add RDF4J driver (renaming of Sesame driver, which has been deprecated and will be removed in the future)
• 0.17.0 - Support for SPARQL-based entity attributes and Criteria API. See the wiki for more details.

See CHANGELOG.md for detailed change history.

References

• [1] J. Tao and E. Sirin, J. Bao, D. L. McGuinness, Integrity Constraints in OWL, The Twenty-Fourth AAAI Conference on Artificial Intelligence, 2010, available online at https://ojs.aaai.org/index.php/AAAI/article/view/7525/7386
• [2] JSR 338 http://jcp.org/en/jsr/detail?id=338
• [3] The Java Language Specification, Java SE 8 Edition https://docs.oracle.com/javase/specs/jls/se8/html/index.html
• [4] P. Křemen and Z. Kouba: Ontology-Driven Information System Design. IEEE Transactions on Systems, Man, and Cybernetics: Part C, 42(3):334–344, May 2012 https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6011704
• [5] M. Ledvinka and P. Křemen: JOPA: Accessing Ontologies in an Object-oriented Way. In Proceedings of the 17th International Conference on Enterprise Information Systems. Porto: SciTePress - Science and Technology Publications, 2015, p. 212-222. ISBN 978-989-758-096-0. http://www.scitepress.org/DigitalLibrary/PublicationsDetail.aspx?ID=p/CdcFwtlFM=&t=1
• [6] M. Ledvinka and P. Křemen and B. Kostov: JOPA: Efficient Ontology-based Information System Design In: The Semantic Web: ESWC 2016 Satellite Events. Cham: Springer International Publishing AG, 2016. pp. 156-160. 9989. ISSN 0302-9743. ISBN 978-3-319-47601-8. ESWC 2016 Demo
• [7] M. Ledvinka and P. Křemen: A comparison of object-triple mapping libraries Semantic Web, 2019, doi: 10.3233/SW-190345

License

LGPLv3