Hierarchical Synonym Type Demo

README.md

Hierarchical Synonym Type Demo

This demonstration goes along with information-artifact-ontology/ontology-metadata#194 to show what happens when ROBOT tries to convert an ontology that has hierarchical synonym type properties.

Unfortunately, it doesn't appear to write the child property in OBO. This is probably because the parser only looks for direct children of oboInOwl:SynonymTypeProperty

hierarchical-synonym-type-demo.obo

format-version: 1.2
synonymtypedef: OMO:0003000 "abbreviation"
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# 
ontology: http://www.semanticweb.org/cthoyt/ontologies/2025/8/untitled-ontology-153
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003000>))\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/OMO_0003012>))\n############################\n#   Annotation Properties\n############################\n\n# Annotation Property: <http://purl.obolibrary.org/obo/OMO_0003012> (<http://purl.obolibrary.org/obo/OMO_0003012>)\n\nSubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/OMO_0003012> <http://purl.obolibrary.org/obo/OMO_0003000>)\n\n\n)

[Term]
id: http://purl.obolibrary.org/obo/IDPO_89a27cc2_0d50_4b43_8dcc_d9bbd29704eb
name: example class
synonym: "EC" EXACT OMO:0003012 []

hierarchical-synonym-type-demo.owl

<?xml version="1.0"?>
<rdf:RDF xmlns="http://www.semanticweb.org/cthoyt/ontologies/2025/8/untitled-ontology-153/"
     xml:base="http://www.semanticweb.org/cthoyt/ontologies/2025/8/untitled-ontology-153/"
     xmlns:obo="http://purl.obolibrary.org/obo/"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
    <owl:Ontology rdf:about="http://www.semanticweb.org/cthoyt/ontologies/2025/8/untitled-ontology-153"/>

    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003000">
        <rdfs:label xml:lang="en">abbreviation</rdfs:label>
        <rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
    </owl:AnnotationProperty>
    
    <owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/OMO_0003012">
        <rdfs:label xml:lang="en">acronym</rdfs:label>
        <rdfs:subPropertyOf rdf:resource="http://purl.obolibrary.org/obo/OMO_0003000"/>
    </owl:AnnotationProperty>
    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
    <owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasSynonymType"/>
    
    <owl:Class rdf:about="http://purl.obolibrary.org/obo/IDPO_89a27cc2_0d50_4b43_8dcc_d9bbd29704eb">
        <oboInOwl:hasExactSynonym>EC</oboInOwl:hasExactSynonym>
        <rdfs:label xml:lang="en">example class</rdfs:label>
    </owl:Class>
    
    <owl:Axiom>
        <owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/IDPO_89a27cc2_0d50_4b43_8dcc_d9bbd29704eb"/>
        <owl:annotatedProperty rdf:resource="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym"/>
        <owl:annotatedTarget>EC</owl:annotatedTarget>
        <oboInOwl:hasSynonymType rdf:resource="http://purl.obolibrary.org/obo/OMO_0003012"/>
    </owl:Axiom>
</rdf:RDF>

This only works I guess because of the owl-axioms header which is killed by many OBO-fication processes.. So I think your demo proves we cannot do what you want at the moment..

You will have to file an issue here:

https://github.com/owlcollab/oboformat/issues?q=is%3Aissue%20state%3Aopen%20synonym%20type

And keep fingers crossed. Sorry!

for now ;)

we'll get there