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DOI

KGCL Java - KGCL library for Java and ROBOT

KGCL-Java is an implementation of the Knowledge Graph Change Language (KGCL) specification for the Java language – just a hobby, won’t be big and professional like the INCATools implementation.

Design

The code is organized in four distinct packages.

The org.incenp.obofoundry.kgcl package is intended to provide a reasonably high-level API to serialise, deserialise, and manipulate KGCL objects.

The org.incenp.obofoundry.kgcl.model package provides the classes that make up the object model for KGCL. Those classes are directly derived from the LinkML schema that formally describes KGCL (they are generated from a custom LinkML-based generator). Those classes may be used by those who want to manipulate KGCL objects.

The org.incenp.obofoundry.kgcl.owl package provides classes to apply KGCL-described changes to a OWL ontology using the OWLAPI.

The org.incenp.obofoundry.kgcl.parser package contains an ANTLR-generated parser to convert KGCL instructions into a corresponding object representation. The classes there may be used by those who want to parse KGCL and manipulate the parse tree themselves (knowledge of the ANTLR runtime library is needed).

Library API

Parsing a KGCL file

Use the org.incenp.obofoundry.kgcl.KGCLReader to parse a KGCL file:

import org.incenp.obofoundry.kgcl.KGCLReader;
import org.incenp.obofoundry.kgcl.model.Change;
import java.util.List;

KGCLReader reader = new KGCLReader([filename, file, InputStream, or Reader object]);
if ( reader.read() ) {
    // File successfully parsed
    List<Change> changes = read.getChangeset();
} else {
    // Syntax errors found
    for ( KGCLSyntaxError error : reader.getErrors() ) {
        System.err.printf("syntax error %s\n", error.toString());
    }
}

The reader will throw the standard exceptions (FileNotFoundException, IOException) if some non-KGCL-related I/O errors occur.

Before attempting to read, you can pass a OWLAPI PrefixManager to the reader, which will use it to expand CURIEs in the KGCL file. For example, assuming you have an ontology in a file format that supports prefixes:

OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
OWLOntology o = mgr.loadOntologyFrom...;
reader.setPrefixManager(mgr.getOntologyFormat(o).asPrefixOWLOntologyFormat());

Writing a KGCL file

Use the org.incenp.obofoundry.kgcl.KGCLWriter to serialise KGCL change objects into the KGCL language:

import org.incenp.obofoundry.kgcl.KGCLWriter
import org.incenp.obofoundry.kgcl.model.Change;

KGCLWriter writer = new KGCLWriter([filename, file, or OutputStream object]);
writer.write(change); // write an individual change;
writer.write(changes); // write several changes in one step,
                       // changes is a List<Change>
writer.close();

The writer will throw standard I/O exceptions upon I/O errors.

As for parsing, you can pass a OWL API PrefixManager to the writer to condense identifiers into short, “CURIEfied” identifiers.

Applying the changes to a OWL ontology

Use the org.incenp.obofoundry.kgcl.owl.OntologyPatcher to apply changes to an ontology:

import org.incenp.obofoundry.kgcl.RejectedChange;
import org.incenp.obofoundry.kgcl.model.Change;
import org.incenp.obofoundry.kgcl.owl.OntologyPatcher;
import org.semanticweb.owlapi.model.OWLOntology;
import java.util.List;

OWLOntology o = ...;
List<Change> changes = ...;
OWLReasoner reasoner = ...;
OntologyPatcher patcher = new OntologyPatcher(o, reasoner);
if ( patcher.apply(changes, false) ) {
    // All changes were applied
    o.saveOntology(...);
} else {
    // Some changes could not be applied
    for ( RejectedChange rc : patcher.getRejectedChanges() ) {
        System.err.printf("Change rejected: %s\n", rc.getReason());
    }
}

ROBOT command

KGCL-Java provides a ROBOT command apply that is intended to allow the injection of KGCL instructions as part of a ROBOT pipeline.

To enable it, install the release artefact kcgl-robot-plugin-X.Y.Z.jar in a directory where ROBOT (1.9.5 minimum) searches for plugins, and rename it to a shorter name such as kgcl.jar.

Building KGCL with the standard Maven goal package will also produce a Jar file that includes ROBOT and that may be used as a standalone version of ROBOT, where the apply command is available as a built-in command (in addition to all the standard commands).

The apply command takes a single KGCL instruction in its -k (or --kgcl) option, or a KGCL file (with one instruction per line) in its -K (or --kgcl-file) option, and apply the requested changes to the current ontology. Both options can be used repeatedly.

robot apply -i input.ofn -K changes.kgcl -o output.ofn

If some changes cannot be applied because they don’t match the contents of the ontology (for example, trying to add a label to a class that does not exist), they will be written back to a file with the same name as the original KGCL file, with a ".rej" extension appended.

If the --no-partial-apply option is used, then the command will refuse to apply any changes if at least one change cannot be applied.

Todo

KGCL implementation chart (parsed means the library can recognize the instruction and convert it to its object representation; applied means the library can apply the change to an ontology):

Change type Parsed Applied
rename yes yes
create class yes yes
obsolete yes yes
delete yes yes
move yes yes
unobsolete yes yes
deepen yes yes
shallow yes yes
change relationship yes yes
change annotation yes yes
create edge yes yes
delete edge yes yes
create synonym yes yes
remove synonym yes yes
change synonym yes yes
remove from subset yes yes
add to subset yes yes
add definition yes yes
change definition yes yes
remove definition yes yes

Homepage and repository

The project is located at https://incenp.org/dvlpt/kgcl-java/. The source code is available in a Git repository at https://github.com/gouttegd/kgcl-java.

Copying

KGCL-Java is distributed under the terms of the GNU General Public License, version 3 or higher. The full license is included in the COPYING file of the source distribution.

KGCL-Java includes code that is automatically derived from the KGCL schema (all classes under the org.incenp.obofoundry.kgcl.model namespace). That code is distributed under the same terms as the schema itself:

Copyright (c) 2022 Mark A. Miller

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.