SSSOM Java - SSSOM library for Java

SSSOM-Java is an implementation of the Simple Standard for Sharing Ontology Mappings (SSSOM) specification for the Java language – just a hobby, won’t be big and professional like sssom-py.

The project provides a Java library that can be used to support the SSSOM standard in a Java application, a program to manipulate mapping sets from the command line, and a pluggable command for the ROBOT ontology manipulation tool.

Features

• Reading a SSSOM mapping set from the TSV serialisation format.

import org.incenp.obofoundry.sssom.model.MappingSet;
import org.incenp.obofoundry.sssom.model.Mapping;
import org.incenp.obofoundry.sssom.TSVReader;
import org.incenp.obofoundry.sssom.SSSOMFormatException;

[...]
MappingSet mappingSet;
try {
    TSVReader reader = new TSVReader("my-mappings.sssom.tsv");
    mappingSet = reader.read();
} catch (SSSOMFormatException e) {
    // Invalid SSSOM data
    return;
}

// play with the mapping set
for (Mapping m : mappingSet.getMappings()) {
    System.out.printf("%s -[%s]-> %s\n", m.getSubjectId(), \
                                         m.getPredicateId(), \
                                         m.getObjectId());
}

• Writing a SSSOM mapping set to the TSV serialisation format.

import org.incenp.obofoundry.sssom.model.MappingSet;
import org.incenp.obofoundry.sssom.TSVWriter;

[...]
MappingSet mappingSet = ...;
try {
    TSVWriter writer = new TSVWriter("my-mappings.sssom.tsv");
    writer.write(mappingSet);
} catch (IOException e) {
    // I/O error
}

• Reading/writing a mapping set from/to the JSON serialisation format.

• Reading/writing a mapping set from/to the RDF/Turtle serialisation format.

• Extracting SSSOM mappings from a OWL ontology with ROBOT:

robot sssom:xref-extract -i uberon.owl --mapping-file uberon-mappings.sssom.tsv

By default, this honours the oboInOwl:treat-xrefs-as-... annotations found in the ontology (contrary to sssom parse or runoak mappings).

• Injecting arbitrary axioms into a OWL ontology with ROBOT, with the axioms to inject being described by rules written in an ad-hoc SSSOM/Transform language. As an example, here is how to use it to generate bridging axioms between the Drosophila Anatomy Ontology (FBbt) and the taxon-neutral ontologies UBERON and CL:

subject==FBbt:* (object==CL:* || object==UBERON:*) {
    predicate==semapv:crossSpeciesExactMatch -> {
        create_axiom("%subject_id EquivalentTo: %object_id and (BFO:0000050 some NCBITaxon:7227)");
        annotate(%{subject_id}, IAO:00000589, "%{subject_label} (Drosophila)");
    }
}

Assuming this is written in a file named bridge.rules, one can then generate a merged ontology between FBbt, UBERON, and CL as follows:

robot merge -i uberon.owl -i cl.owl -i fbbt.owl \
      sssom:inject --sssom fbbt-mappings.sssom.tsv \
                   --ruleset bridge.rules \
      annotate --ontology-iri http://purl.obolibrary.org/obo/bridged.owl \
               --output bridged.owl

• Renaming entities within a OWL ontology, using a SSSOM mapping set as the source of truth for which entity should be renamed and into what.

• Manipulating mapping sets from the command line, with a dedicated command-line tool named sssom-cli.

Building

Build by running mvn clean package. This will produce five distinct Jar files:

• sssom-core-x.y.z.jar (in core/target): a minimal Java library, containing only the classes implementing the SSSOM specification.
• sssom-ext-x.y.z.jar (in ext/target): an extended library, built on top of sssom-core and providing more classes to facilitate the manipulation of mappings.
• sssom-robot-plugin-x.y.z.jar (in robot/target): a file usable as a ROBOT plugin.
• sssom-robot-standalone-x.y.z.jar (in robot/target): a standalone version of ROBOT (1.9.6), which includes the command(s) from the SSSOM plugin as if they were built-in commands.
• sssom-cli-x.y.z.jar (in cli/target): the sssom-cli command-line tool, as a self-sufficient executable Jar archive.

To use the library in a Java project, use the following identifiers:

• group ID: org.incenp;
• artifact ID: sssom-core for the core library, or sssom-ext for extended library (which will bring in sssom-core as a dependency).

Homepage and repository

The project is located at https://incenp.org/dvlpt/sssom-java/, where some documentation is also hosted. The source code is available in a Git repository at https://github.com/gouttegd/sssom-java.

Copying

SSSOM-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.