Ocelliless - Tests driver for OWL ontologies

Ocelliless is a tool intended to facilitate “unit-testing” of OWL ontologies. It attempts to test an ontology by repeatedly merging it with a series of “test ontologies” and reasoning over the product of each merge. A test is said to “pass” if it produces a consistent ontology with no unsatisfiable classes when merged with the main ontology.

The name comes from the Drosophila melanogaster gene ocelliless, which is also known as orthodenticle or otd. Here, Ocelliless is an “Ontology Tests Driver” or “OTD”.

Installation

Build the program with Maven by running, from the source directory:

$ mvn clean package

This will produce a file ocelliless-X.Y.Z-jar-with-dependencies.jar in the target subdirectory.

Run the program with:

$ java -jar target/ocelliless-X.Y.Z-jar-with-dependencies.jar

Basic usage

A “unit test” looks like the following:

@prefix : <http://purl.obolibrary.org/obo/fbbt/tests/test2.ttl#test_> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix odt: <https://incenp.org/ocelliless/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .

<http://purl.obolibrary.org/obo/fbbt/tests/test2.ttl> rdf:type owl:Ontology ;
                                                      odt:target obo:FBbt_00007004 .

:001 rdf:type owl:Class ;
     rdfs:subClassOf [ rdf:type owl:Restriction ;
                       owl:onProperty obo:BFO_0000050 ;
                       owl:someValuesFrom obo:FBbt_00004928
                     ] ,
                     [ rdf:type owl:Restriction ;
                       owl:onProperty obo:BFO_0000050 ;
                       owl:someValuesFrom obo:FBbt_00007004
                     ] ;
     rdfs:label "part_of testis is part_of male organism"^^xsd:string ;
     obo:IAO_0000115 "Something that is part of the testis should be part of a male organism."^^xsd:string .

This test checks the Drosophila Anatomy Ontology (FBbt) to ensure that any class that is part_of a male-specific structure (here, the testis, FBbt:00004928) is automatically classified as part_of a male organism (FBbt:00007004).

Here is another test (not repeating the prefixes, for brevity) that checks that something cannot be simultaneously part_of the larva (FBbt:00001727) and part_of the adult (FBbt:00003004) – this is an example of a “expected failure” (XFAIL): merging this with the FBbt ontology is supposed to produce an unsatisfiable class (so the test will actually fail if it does not produce it):

<http://purl.obolibrary.org/obo/fbbt/tests/test1.ttl> rdf:type owl:Ontology ;
                                                      odt:target obo:FBbt_00001127 ;
                                                      odt:xfail "yes"^^xsd:string .

:001 rdf:type owl:Class ;
     rdfs:subClassOf [ rdf:type owl:Restriction ;
                       owl:onProperty obo:BFO_0000050 ;
                       owl:someValuesFrom obo:FBbt_00001727
                     ] ,
                     [ rdf:type owl:Restriction ;
                       owl:onProperty obo:BFO_0000050 ;
                       owl:someValuesFrom obo:FBbt_00003004
                     ] ;
     rdfs:label "larval - adult mix up"^^xsd:string ;
     obo:IAO_0000115 "A class that is both part_of some larva and part_of some adult - should be unsatisfiable."^^xsd:string .

Run those two tests against the released version of FBbt:

$ java -jar ocelliless-0.0.1-SNAPSHOT-jar-with-dependencies.jar \
  -c annotations.ofn -i fbbt-full.owl tests/test1.ttl tests/test2.ttl
ocelliless: Test 1/2 (tests/test1.ttl): PASS
ocelliless: Test 2/2 (tests/test2.ttl): PASS
ocelliless: fbbt.owl: 2/2 tests passed
ocelliless: Saving annotations component to annotations.ofn

Here, both tests have passed. The file annotations.ofn contains annotations that can be merged into the tested ontology to add links pointing to the test files (assuming they are published alongside the ontology itself):

Prefix(owl:=<http://www.w3.org/2002/07/owl#>)
Prefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)
Prefix(xml:=<http://www.w3.org/XML/1998/namespace>)
Prefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)
Prefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)


Ontology(
Declaration(AnnotationProperty(<https://incenp.org/ocelliless/test>))

AnnotationAssertion(<https://incenp.org/ocelliless/test> <http://purl.obolibrary.org/obo/FBbt_00001127> <http://purl.obolibrary.org/obo/fbbt/tests/test1.ttl>)
AnnotationAssertion(<https://incenp.org/ocelliless/test> <http://purl.obolibrary.org/obo/FBbt_00007004> <http://purl.obolibrary.org/obo/fbbt/tests/test2.ttl>)
)

Copying

Ocelliless 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.

Repository

The latest source code is available in a Git repository at https://github.com/gouttegd/ocelliless.