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balhoff
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Allow arbitrary annotation properties as qualifier tags in OBO #1099
Allowing arbitrary defined annotation properties as qualifier tags. Use oboInOWL as the default namespace when looking up tag IRIs. This helps with backwards compatibility for undeclared annotation properties. Enforce oio namespace for created_by and creation_date.
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‎contract/src/test/java/org/obolibrary/oboformat/TagIRIsTest.java

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package org.obolibrary.oboformat;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.util.Collections;
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import java.util.Set;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.junit.jupiter.api.Test;
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import org.semanticweb.owlapi.api.test.baseclasses.TestBase;
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import org.semanticweb.owlapi.model.IRI;
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import org.semanticweb.owlapi.model.OWLAnnotation;
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import org.semanticweb.owlapi.model.OWLAnnotationProperty;
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import org.semanticweb.owlapi.model.OWLAxiom;
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import org.semanticweb.owlapi.model.OWLClass;
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import org.semanticweb.owlapi.model.OWLLiteral;
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import org.semanticweb.owlapi.model.OWLOntology;
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import org.semanticweb.owlapi.vocab.OWL2Datatype;
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class TagIRIsTest extends TestBase {
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@Test
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void testTagIRIMapping() {
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OWLAnnotationProperty definition =
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df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/IAO_0000115"));
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OWLAnnotationProperty oioCreatedBy = df.getOWLAnnotationProperty(
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IRI.create("http://www.geneontology.org/formats/oboInOwl#created_by"));
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OWLAnnotationProperty oioInventedBy = df.getOWLAnnotationProperty(
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IRI.create("http://www.geneontology.org/formats/oboInOwl#invented_by"));
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OWLAnnotationProperty source =
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df.getOWLAnnotationProperty(IRI.create("http://purl.obolibrary.org/obo/MYONT_20"));
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OWLOntology ont = loadOntology("obo/tag_iris.obo", m);
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Set<OWLAxiom> axioms = ont.getAxioms();
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OWLClass term1 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_1"));
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OWLClass term2 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_2"));
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OWLClass term3 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_3"));
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OWLClass term4 = df.getOWLClass(IRI.create("http://purl.obolibrary.org/obo/MYONT_4"));
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Set<OWLAnnotation> annotations = Stream
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.of(df.getOWLAnnotation(df.getRDFSComment(), string("Here is a sub-annotation.")),
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df.getOWLAnnotation(df.getRDFSSeeAlso(), string("A nested see also value.")))
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.collect(Collectors.toSet());
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assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term1.getIRI(),
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string("Definition of term one."), annotations)));
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assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(df.getRDFSSeeAlso(),
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term1.getIRI(), string("See also value."))));
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assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term2.getIRI(),
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string("Definition of term two."), Collections
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.singleton(df.getOWLAnnotation(source, string("A nested annotation value."))))));
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assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term3.getIRI(),
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string("Definition of term three."), Collections
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.singleton(df.getOWLAnnotation(source, string("A definition source value."))))));
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assertTrue(
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axioms.contains(
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df.getOWLAnnotationAssertionAxiom(oioCreatedBy, term3.getIRI(), string("goc:bro"))),
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"created_by is built in and should not be overridden by a typedef");
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assertTrue(
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axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term4.getIRI(),
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string("Definition of term four."),
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Collections
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.singleton(df.getOWLAnnotation(oioInventedBy, string("An inventor value."))))),
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"An undeclared tag should have oio namespace");
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}
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protected OWLLiteral string(String l) {
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return df.getOWLLiteral(l, OWL2Datatype.XSD_STRING);
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}
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}

‎contract/src/test/resources/obo/tag_iris.obo

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format-version: 1.2
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ontology: myont
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[Term]
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id: MYONT:1
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name: term one
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def: "Definition of term one." [] {comment="Here is a sub-annotation.", seeAlso="A nested see also value."}
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property_value: seeAlso "See also value." xsd:string
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[Term]
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id: MYONT:2
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name: term two
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def: "Definition of term two." [] {MYONT:20="A nested annotation value."}
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property_value: MYONT:21 "A top level annotation value." xsd:string
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[Term]
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id: MYONT:3
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name: term three
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def: "Definition of term three." [] {source="A definition source value."}
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intersection_of: MYONT:2 ! term two
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intersection_of: results_in_transport_across GO:0005739 ! mitochondrion
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created_by: goc:bro
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[Term]
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id: MYONT:4
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name: term four
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def: "Definition of term four." [] {invented_by="An inventor value."}
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[Typedef]
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id: source
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name: source
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xref: MYONT:20
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is_metadata_tag: true
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[Typedef]
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id: MYONT:21
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name: source2
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is_metadata_tag: true
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[Typedef]
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id: seeAlso
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name: see also
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xref: http://www.w3.org/2000/01/rdf-schema#seeAlso
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is_metadata_tag: true
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[Typedef]
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id: results_in_transport_across
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name: results in transport across
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namespace: external
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xref: RO:0002342
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[Typedef]
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id: created_by
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name: created by
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namespace: external
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xref: http://purl.org/dc/terms/creator

‎oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java

Lines changed: 31 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,7 @@
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package org.obolibrary.obo2owl;
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import static org.obolibrary.obo2owl.Obo2OWLConstants.DEFAULT_IRI_PREFIX;
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import static org.obolibrary.obo2owl.Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
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import static org.semanticweb.owlapi.util.OWLAPIPreconditions.verifyNotNull;
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import java.io.File;
@@ -1518,6 +1519,15 @@ public static IRI trTagToIRI(String tag) {
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return iri;
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}
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1522+
@Nonnull
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private IRI trTagToIRIIncludingTypedefs(String tag) {
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IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
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if (iri == null) {
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iri = oboIdToIRI(tag, true);
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}
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return iri;
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}
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15211531
/**
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* Translate tag to annotation prop.
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*
@@ -1526,7 +1536,7 @@ public static IRI trTagToIRI(String tag) {
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*/
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@Nonnull
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protected OWLAnnotationProperty trTagToAnnotationProp(@Nonnull String tag) {
1529-
IRI iri = trTagToIRI(tag);
1539+
IRI iri = trTagToIRIIncludingTypedefs(tag);
15301540
OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
15311541
if (!apToDeclare.contains(ap)) {
15321542
apToDeclare.add(ap);
@@ -1624,22 +1634,31 @@ protected OWLAnnotationValue trLiteral(@Nonnull Object inputValue) {
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*/
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@Nonnull
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public IRI oboIdToIRI(@Nonnull String id) {
1637+
return oboIdToIRI(id, false);
1638+
}
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1640+
private IRI oboIdToIRI(@Nonnull String id, boolean oboInOwlDefault) {
16271641
IRI iri = idToIRICache.get(id);
16281642
if (iri == null) {
1629-
iri = oboIdToIRI_load(id);
1643+
iri = oboIdToIRI_load(id, oboInOwlDefault);
16301644
idToIRICache.put(id, iri);
16311645
}
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return iri;
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}
16341648

1649+
@Nonnull
1650+
public IRI oboIdToIRI_load(@Nonnull String id) {
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return oboIdToIRI_load(id, false);
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}
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16351654
/**
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* Obo id to iri.
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*
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* @param id the id
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* @return the iri
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*/
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@Nonnull
1642-
public IRI oboIdToIRI_load(@Nonnull String id) {
1661+
public IRI oboIdToIRI_load(@Nonnull String id, boolean oboInOwlDefault) {
16431662
if (id.contains(" ")) {
16441663
LOG.error("id contains space: \"{}\"", id);
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throw new OWLParserException("spaces not allowed: '" + id + '\'');
@@ -1704,10 +1723,16 @@ public IRI oboIdToIRI_load(@Nonnull String id) {
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// if(id.contains("_"))
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// db += "_";
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localId = idParts[0];// Unprefixed-ID
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}
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String uriPrefix = DEFAULT_IRI_PREFIX + db;
1709-
if (idSpaceMap.containsKey(db)) {
1710-
uriPrefix = idSpaceMap.get(db);
1728+
String uriPrefix;
1729+
if (oboInOwlDefault) {
1730+
uriPrefix = OIOVOCAB_IRI_PREFIX;
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} else {
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uriPrefix = DEFAULT_IRI_PREFIX + db;
1733+
if (idSpaceMap.containsKey(db)) {
1734+
uriPrefix = idSpaceMap.get(db);
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}
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}
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String safeId;
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try {

‎oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java

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@@ -1869,6 +1869,8 @@ public static String owlObjectToTag(OWLObject obj) {
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String prefix = Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
18701870
if (iri.startsWith(prefix)) {
18711871
tag = iri.substring(prefix.length());
1872+
} else {
1873+
tag = getIdentifier(iriObj);
18721874
}
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}
18741876
return tag;

‎oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java

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Original file line numberDiff line numberDiff line change
@@ -55,6 +55,9 @@ public enum Obo2OWLVocabulary implements HasIRI {
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/**IRI_IAO_0100001*/ IRI_IAO_0100001(DEFAULT_IRI_PREFIX, "IAO_0100001", "term replaced by", OboFormatTag.TAG_REPLACED_BY.getTag()),
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/**IRI_OIO_shorthand*/ IRI_OIO_shorthand(OIOVOCAB_IRI_PREFIX, "shorthand", "shorthand", "shorthand"),
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/**IRI_OIO_consider*/ IRI_OIO_consider(OIOVOCAB_IRI_PREFIX, "consider", "consider", OboFormatTag.TAG_CONSIDER.getTag()),
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/**IRI_OIO_id*/ IRI_OIO_id(OIOVOCAB_IRI_PREFIX, "id", "id", OboFormatTag.TAG_ID.getTag()),
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/**IRI_OIO_created_by*/ IRI_OIO_created_by(OIOVOCAB_IRI_PREFIX, "created_by", "created by", OboFormatTag.TAG_CREATED_BY.getTag()),
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/**IRI_OIO_creation_date*/ IRI_OIO_creation_date(OIOVOCAB_IRI_PREFIX, "creation_date", "creation date", OboFormatTag.TAG_CREATION_DATE.getTag()),
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/**IRI_OIO_hasOBOFormatVersion*/ IRI_OIO_hasOBOFormatVersion(OIOVOCAB_IRI_PREFIX, "hasOBOFormatVersion", "has_obo_format_version", OboFormatTag.TAG_FORMAT_VERSION.getTag()),
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/**IRI_OIO_treatXrefsAsIsA*/ IRI_OIO_treatXrefsAsIsA(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-is_a", "treat-xrefs-as-is_a", OboFormatTag.TAG_TREAT_XREFS_AS_IS_A.getTag()),
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/**IRI_OIO_treatXrefsAsHasSubClass*/ IRI_OIO_treatXrefsAsHasSubClass(OIOVOCAB_IRI_PREFIX, "treat-xrefs-as-has-subclass", "treat-xrefs-as-has-subclass", OboFormatTag.TAG_TREAT_XREFS_AS_HAS_SUBCLASS.getTag()),

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