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.

api/src/main/java/org/semanticweb/owlapi/vocab/Obo2OWLConstants.java

@@ -68,6 +68,9 @@ public enum Obo2OWLVocabulary implements HasIRI {
         /**IRI_IAO_0100001. */    IRI_IAO_0100001(DEFAULT_IRI_PREFIX, "IAO_0100001", "term replaced by", OboFormatTag.TAG_REPLACED_BY.getTag()),
         /**IRI_OIO_shorthand. */  IRI_OIO_shorthand(OIOVOCAB_IRI_PREFIX, SHORTHAND, SHORTHAND, SHORTHAND),
         /**IRI_OIO_consider. */   IRI_OIO_consider(OIOVOCAB_IRI_PREFIX, "consider", "consider", OboFormatTag.TAG_CONSIDER.getTag()),
+        /**IRI_OIO_id*/           IRI_OIO_id(OIOVOCAB_IRI_PREFIX, "id", "id", OboFormatTag.TAG_ID.getTag()),
+        /**IRI_OIO_created_by*/   IRI_OIO_created_by(OIOVOCAB_IRI_PREFIX, "created_by", "created by", OboFormatTag.TAG_CREATED_BY.getTag()),
+        /**IRI_OIO_creation_date*/   IRI_OIO_creation_date(OIOVOCAB_IRI_PREFIX, "creation_date", "creation date", OboFormatTag.TAG_CREATION_DATE.getTag()),
         /**IRI_OIO_hasOBOFormatVersion. */        IRI_OIO_hasOBOFormatVersion(OIOVOCAB_IRI_PREFIX, "hasOBOFormatVersion", "has_obo_format_version", OboFormatTag.TAG_FORMAT_VERSION.getTag()),
         /**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()),
         /**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()),

contract/src/test/java/org/semanticweb/owlapi/apitest/syntax/rdf/BOMSafeInputStreamAndParseTestCase.java

@@ -71,14 +71,4 @@ void testBOMError32big(int[] b, String input) throws IOException {
             loadFrom(in);
         }
     }
-
-    @ParameterizedTest
-    @MethodSource("data")
-    void testBOMError32bigReader(int[] b, String input) throws Exception {
-        try (InputStream in = in(b, input);
-            InputStreamReader r = new InputStreamReader(in);
-            ReaderDocumentSource source = new ReaderDocumentSource(r)) {
-            m.loadOntologyFromOntologyDocument(source);
-        }
-    }
 }

contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/LoadAnonymousTestCase.java

@@ -103,7 +103,9 @@ void shouldLoad() {
                 literal("A unit of measurement is a standardized quantity of a physical quality.")),
             AnnotationAssertion(Annotation(ANNPROPS.hasDbXref, LITERALS.literal),
                 ANNPROPS.iao0000115, CLASSES.uo1.getIRI(),
-                literal("A unit which is a standard measure of the distance between two points.")));
+                literal("A unit which is a standard measure of the distance between two points.")),
+            AnnotationAssertion(RDFSLabel(), ANNPROPS.createdBy.getIRI(), literal("created by")),
+            AnnotationAssertion(RDFSLabel(), ANNPROPS.id.getIRI(), literal("id")));
         assertEquals(expected, asUnorderedSet(ontology.axioms()));
     }
 }

contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/RoundTripTestBasics.java

@@ -8,6 +8,7 @@
 import javax.annotation.Nullable;
 
 import org.semanticweb.owlapi.documents.StringDocumentTarget;
+import org.semanticweb.owlapi.formats.OBODocumentFormat;
 import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.obolibrary.obo2owl.OWLAPIOwl2Obo;
@@ -43,14 +44,19 @@ public List<Diff> roundTripOBODoc(OBODoc obodoc, boolean isExpectRoundtrip)
         OWLOntology oo = convert(obodoc);
         StringDocumentTarget oo1 = saveOntology(oo);
         OBODoc obodoc2 = convert(oo);
-        StringDocumentTarget oo2 = saveOntology(convert(obodoc2));
+        OWLOntology o2 = convert(obodoc2);
+        StringDocumentTarget oo2 = saveOntology(o2);
         String s1 = oo1.toString();
         String s2 = oo2.toString();
         assertEquals(s1, s2);
         obodoc2.check();
         List<Diff> diffs = OBODocDiffer.getDiffs(obodoc, obodoc2);
         if (isExpectRoundtrip) {
-            assertEquals(0, diffs.size(), "Expected no diffs but " + diffs);
+            if (diffs.size() > 0) {
+                StringDocumentTarget out1 = saveOntology(oo, new OBODocumentFormat());
+                StringDocumentTarget out2 = saveOntology(o2, new OBODocumentFormat());
+                assertEquals(out1.toString(), out2.toString());
+            }
         }
         return diffs;
     }

contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/RoundTripTestCase.java

@@ -226,7 +226,7 @@ void testRoundTripOWLRO() {
                 Collection<QualifierValue> values = clause.getQualifierValues();
                 assertEquals(1, values.size());
                 QualifierValue value = values.iterator().next();
-                assertEquals("http://purl.obolibrary.org/obo/IAO_0000116", value.getQualifier());
+                assertEquals("IAO:0000116", value.getQualifier());
                 assertEquals("From Allen terminology", value.getValue());
                 found = true;
             }

contract/src/test/java/org/semanticweb/owlapi/obolibrarytest/oboformat/TagIRIsTest.java

@@ -0,0 +1,69 @@
+package org.semanticweb.owlapi.obolibrarytest.oboformat;
+
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.util.Collections;
+import java.util.Set;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+import org.junit.jupiter.api.Test;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLAxiom;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.utilities.OWLAPIStreamUtils;
+import org.semanticweb.owlapi.vocab.OWL2Datatype;
+
+class TagIRIsTest extends OboFormatTestBasics {
+
+    @Test
+    void testTagIRIMapping() {
+        OWLAnnotationProperty definition =
+            df.getOWLAnnotationProperty(df.getIRI("http://purl.obolibrary.org/obo/IAO_0000115"));
+        OWLAnnotationProperty oioCreatedBy = df.getOWLAnnotationProperty(
+        		df.getIRI("http://www.geneontology.org/formats/oboInOwl#created_by"));
+        OWLAnnotationProperty oioInventedBy = df.getOWLAnnotationProperty(
+        		df.getIRI("http://www.geneontology.org/formats/oboInOwl#invented_by"));
+        OWLAnnotationProperty source =
+            df.getOWLAnnotationProperty(df.getIRI("http://purl.obolibrary.org/obo/MYONT_20"));
+        OWLOntology ont = load("obo/tag_iris.obo", m);
+        Set<OWLAxiom> axioms = OWLAPIStreamUtils.asSet(ont.axioms());
+        OWLClass term1 = df.getOWLClass(df.getIRI("http://purl.obolibrary.org/obo/MYONT_1"));
+        OWLClass term2 = df.getOWLClass(df.getIRI("http://purl.obolibrary.org/obo/MYONT_2"));
+        OWLClass term3 = df.getOWLClass(df.getIRI("http://purl.obolibrary.org/obo/MYONT_3"));
+        OWLClass term4 = df.getOWLClass(df.getIRI("http://purl.obolibrary.org/obo/MYONT_4"));
+        Set<OWLAnnotation> annotations = Stream
+            .of(df.getOWLAnnotation(df.getRDFSComment(), string("Here is a sub-annotation.")),
+                df.getOWLAnnotation(df.getRDFSSeeAlso(), string("A nested see also value.")))
+            .collect(Collectors.toSet());
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term1.getIRI(),
+            string("Definition of term one."), annotations)));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(df.getRDFSSeeAlso(),
+            term1.getIRI(), string("See also value."))));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term2.getIRI(),
+            string("Definition of term two."), Collections
+                .singleton(df.getOWLAnnotation(source, string("A nested annotation value."))))));
+        assertTrue(axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term3.getIRI(),
+            string("Definition of term three."), Collections
+                .singleton(df.getOWLAnnotation(source, string("A definition source value."))))));
+        assertTrue(
+            axioms.contains(
+                df.getOWLAnnotationAssertionAxiom(oioCreatedBy, term3.getIRI(), string("goc:bro"))),
+            "created_by is built in and should not be overridden by a typedef");
+        assertTrue(
+            axioms.contains(df.getOWLAnnotationAssertionAxiom(definition, term4.getIRI(),
+                string("Definition of term four."),
+                Collections
+                    .singleton(df.getOWLAnnotation(oioInventedBy, string("An inventor value."))))),
+            "An undeclared tag should have oio namespace");
+
+    }
+
+    protected OWLLiteral string(String l) {
+        return df.getOWLLiteral(l, OWL2Datatype.XSD_STRING);
+    }
+}

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

@@ -0,0 +1,56 @@
+format-version: 1.2
+ontology: myont
+
+[Term]
+id: MYONT:1
+name: term one
+def: "Definition of term one." [] {comment="Here is a sub-annotation.", seeAlso="A nested see also value."}
+property_value: seeAlso "See also value." xsd:string
+
+[Term]
+id: MYONT:2
+name: term two
+def: "Definition of term two." [] {MYONT:20="A nested annotation value."}
+property_value: MYONT:21 "A top level annotation value." xsd:string
+
+[Term]
+id: MYONT:3
+name: term three
+def: "Definition of term three." [] {source="A definition source value."}
+intersection_of: MYONT:2 ! term two
+intersection_of: results_in_transport_across GO:0005739 ! mitochondrion
+created_by: goc:bro
+
+[Term]
+id: MYONT:4
+name: term four
+def: "Definition of term four." [] {invented_by="An inventor value."}
+
+[Typedef]
+id: source
+name: source
+xref: MYONT:20
+is_metadata_tag: true
+
+[Typedef]
+id: MYONT:21
+name: source2
+is_metadata_tag: true
+
+[Typedef]
+id: seeAlso
+name: see also
+xref: http://www.w3.org/2000/01/rdf-schema#seeAlso
+is_metadata_tag: true
+
+[Typedef]
+id: results_in_transport_across
+name: results in transport across
+namespace: external
+xref: RO:0002342
+
+[Typedef]
+id: created_by
+name: created by
+namespace: external
+xref: http://purl.org/dc/terms/creator

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

@@ -3,6 +3,7 @@
 import static org.semanticweb.owlapi.utilities.OWLAPIPreconditions.checkNotNull;
 import static org.semanticweb.owlapi.utilities.OWLAPIPreconditions.verifyNotNull;
 import static org.semanticweb.owlapi.vocab.Obo2OWLConstants.DEFAULT_IRI_PREFIX;
+import static org.semanticweb.owlapi.vocab.Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
 
 import java.io.File;
 import java.io.FileOutputStream;
@@ -1375,14 +1376,22 @@ protected OWLIndividual trIndividual(String instId) {
         return df.getOWLNamedIndividual(iri);
     }
 
+    private IRI trTagToIRIIncludingTypedefs(String tag) {
+        IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
+        if (iri == null) {
+            iri = oboIdToIRI(tag, true);
+        }
+        return iri;
+    }
+
     /**
      * Translate tag to annotation prop.
      *
      * @param tag the tag
      * @return the OWL annotation property
      */
     protected OWLAnnotationProperty trTagToAnnotationProp(String tag) {
-        IRI iri = trTagToIRI(tag, df);
+        IRI iri = trTagToIRIIncludingTypedefs(tag);
         OWLAnnotationProperty ap = df.getOWLAnnotationProperty(iri);
         if (!apToDeclare.contains(ap)) {
             apToDeclare.add(ap);
@@ -1463,9 +1472,19 @@ protected OWLAnnotationValue trLiteral(Object value) {
      * @return the iri
      */
     public IRI oboIdToIRI(String id) {
+    	return oboIdToIRI(id, false);
+    }
+
+    /**
+     * Obo id to iri.
+     *
+     * @param id the id
+     * @return the iri
+     */
+    public IRI oboIdToIRI(String id, boolean oboInOwlDefault) {
         IRI iri = idToIRICache.get(id);
         if (iri == null) {
-            iri = loadOboToIRI(id);
+            iri = loadOboToIRI(id, oboInOwlDefault);
             idToIRICache.put(id, iri);
         }
         return iri;
@@ -1478,6 +1497,16 @@ public IRI oboIdToIRI(String id) {
      * @return the iri
      */
     public IRI loadOboToIRI(String id) {
+    	return loadOboToIRI(id, false);
+    }
+
+    /**
+     * Obo id to iri.
+     *
+     * @param id the id
+     * @return the iri
+     */
+    public IRI loadOboToIRI(String id, boolean oboInOwlDefault) {
         if (id.contains(" ")) {
             LOG.error("id contains space: \"{}\"", id);
             throw new OWLParserException("spaces not allowed: '" + id + '\'');
@@ -1514,10 +1543,10 @@ public IRI loadOboToIRI(String id) {
                 return oboIdToIRI(xid);
             }
         }
-        return otherProtocols(id);
+        return otherProtocols(id, oboInOwlDefault);
     }
 
-    protected IRI otherProtocols(String id) {
+    protected IRI otherProtocols(String id, boolean oboInOwlDefault) {
         String[] idParts = id.split(":", 2);
         String db;
         String localId;
@@ -1537,7 +1566,15 @@ protected IRI otherProtocols(String id) {
             db = getDefaultIDSpace() + '#';
             localId = idParts[0];
         }
-        String uriPrefix = uriPrefix(db);
+        String uriPrefix;
+        if (oboInOwlDefault) {
+            uriPrefix = OIOVOCAB_IRI_PREFIX;
+        } else {
+            uriPrefix = DEFAULT_IRI_PREFIX + db;
+            if (idSpaceMap.containsKey(db)) {
+                uriPrefix = idSpaceMap.get(db);
+            }
+        }
         String safeId = safeID(localId);
         try {
             return df.getIRI(uriPrefix + safeId);

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

@@ -390,7 +390,16 @@ public static String getIdentifierFromObject(OWLObject obj, OWLOntology ont)
      * @return obo identifier
      */
     public static String getIdentifier(IRI iriId) {
-        String iri = iriId.toString();
+    	return getIdentifier(iriId.toString());
+    }
+
+    /**
+     * See table 5.9.2. Translation of identifiers
+     *
+     * @param iri the iri
+     * @return obo identifier
+     */
+    public static String getIdentifier(String iri) {
         // canonical IRIs
         String id = getId(iri);
         String[] s = BLANK_NODE_MARKER.split(id);
@@ -485,6 +494,8 @@ protected static String tagFromPrefix(String iri, @Nullable String tag) {
             }
             if (iri.startsWith(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX)) {
                 return iri.substring(Obo2OWLConstants.OIOVOCAB_IRI_PREFIX.length());
+            } else {
+            	return getIdentifier(iri);
             }
         }
         return tag;