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Allow arbitrary defined annotation properties as qualifier tags in OBO format #1099

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Allow arbitrary defined annotation properties as qualifier tags in OBO format #1099

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778808b
First pass allowing arbitrary defined annotation properties as qualif…
balhoff Mar 3, 2023
e5820ba
Fix copy/paste typo.
balhoff Mar 3, 2023
04183b8
Use oboInOWL as the default namespace when looking up tag IRIs. This …
balhoff Mar 14, 2023
c530f3f
Enforce oio namespace for created_by and creation_date.
balhoff Mar 14, 2023
5242838
Add test cases for OBO tag IRIs.
balhoff Mar 14, 2023
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11 changes: 10 additions & 1 deletion oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIObo2Owl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1518,6 +1518,15 @@ public static IRI trTagToIRI(String tag) {
return iri;
}

@Nonnull
private IRI trTagToIRIIncludingTypedefs(String tag) {
IRI iri = ANNOTATIONPROPERTYMAP.get(tag);
if (iri == null) {
iri = oboIdToIRI(tag);
}
return iri;
}

/**
* Translate tag to annotation prop.
*
Expand All @@ -1526,7 +1535,7 @@ public static IRI trTagToIRI(String tag) {
*/
@Nonnull
protected OWLAnnotationProperty trTagToAnnotationProp(@Nonnull String tag) {
IRI iri = trTagToIRI(tag);
IRI iri = trTagToIRIIncludingTypedefs(tag);
OWLAnnotationProperty ap = fac.getOWLAnnotationProperty(iri);
if (!apToDeclare.contains(ap)) {
apToDeclare.add(ap);
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2 changes: 2 additions & 0 deletions oboformat/src/main/java/org/obolibrary/obo2owl/OWLAPIOwl2Obo.java
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Expand Up @@ -1869,6 +1869,8 @@ public static String owlObjectToTag(OWLObject obj) {
String prefix = Obo2OWLConstants.OIOVOCAB_IRI_PREFIX;
if (iri.startsWith(prefix)) {
tag = iri.substring(prefix.length());
} else {
tag = getIdentifier(iriObj);
}
}
return tag;
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1 change: 1 addition & 0 deletions oboformat/src/main/java/org/obolibrary/obo2owl/Obo2OWLConstants.java
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Expand Up @@ -55,6 +55,7 @@ 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_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()),
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