public static Map<EdamUri, Concept> load(String edamPath) throws OWLOntologyCreationException {
OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
OWLOntology ontology = manager.loadOntologyFromOntologyDocument(new File(edamPath));
String prefix = ontology.getOntologyID().getOntologyIRI().get().toString();
return ontology
.classesInSignature()
.filter(c -> EdamUri.isEdamUri(c.getIRI().toString(), prefix))
.collect(
Collectors.toMap(
c -> new EdamUri(c.getIRI().toString(), prefix),
c -> {
Concept concept = new Concept();
EntitySearcher.getAnnotations(c, ontology)
.forEachOrdered(
a -> {
if (a.getProperty().isLabel())
concept.setLabel(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isDeprecated()) concept.setObsolete(true);
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasExactSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addExactSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addNarrowSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym")
&& a.getValue().asLiteral().isPresent())
concept.addBroadSynonym(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty()
.toStringID()
.equals(
"http://www.geneontology.org/formats/oboInOwl#hasDefinition")
&& a.getValue().asLiteral().isPresent())
concept.setDefinition(a.getValue().asLiteral().get().getLiteral());
else if (a.getProperty().isComment()
&& a.getValue().asLiteral().isPresent())
concept.setComment(a.getValue().asLiteral().get().getLiteral());
});
if (concept.getLabel().isEmpty())
throw new IllegalStateException(
String.format("Label of concept %s is empty", c.getIRI()));
return concept;
},
(u, v) -> {
throw new IllegalStateException(String.format("Duplicate key %s", u));
},
LinkedHashMap::new));
}
private void assertSameConcept(Concept expected, Concept actual, List<String> traversedUrns) {
String errMsg = String.format("%1$s != %2$s", expected, actual);
Assert.assertEquals(errMsg, expected, actual);
Assert.assertEquals(errMsg, expected.getLabel(), actual.getLabel());
Assert.assertEquals(errMsg, expected.getPreferredLabel(), actual.getPreferredLabel());
Assert.assertEquals(errMsg, expected.isHref(), actual.isHref());
Assert.assertEquals(errMsg, expected.getDefinition(), actual.getDefinition());
// To deal with cycles in the hierarchy
if (traversedUrns.contains(expected.getUrn())) {
return;
} else {
traversedUrns.add(expected.getUrn());
}
assertSameConcept(expected.getBroader(), actual.getBroader(), traversedUrns);
assertSameConcept(expected.getNarrower(), actual.getNarrower(), traversedUrns);
assertSameConcept(expected.getRelated(), actual.getRelated(), traversedUrns);
}
