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GO-base does not follow spec #29531

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matentzn opened this issue Jan 11, 2025 · 2 comments · Fixed by #29532
Closed

GO-base does not follow spec #29531

matentzn opened this issue Jan 11, 2025 · 2 comments · Fixed by #29532
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@matentzn
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cc @balhoff

Base spec:

https://oboacademy.github.io/obook/reference/base-specification/

For my use cases the important part that is not respected is missing relax, eg:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0007507">
        <owl:equivalentClass>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0048856"/>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0002296"/>
                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/UBERON_0007100"/>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </owl:equivalentClass>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0032502"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0048513"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/GO_0072359"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <obo:IAO_0000115>The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.</obo:IAO_0000115>
        <obo:RO_0002175 rdf:resource="http://purl.obolibrary.org/obo/NCBITaxon_7227"/>
        <oboInOwl:hasAlternativeId>GO:0007511</oboInOwl:hasAlternativeId>
        <oboInOwl:hasDbXref>Wikipedia:Heart_development</oboInOwl:hasDbXref>
        <oboInOwl:hasNarrowSynonym>dorsal vessel development</oboInOwl:hasNarrowSynonym>
        <oboInOwl:hasOBONamespace>biological_process</oboInOwl:hasOBONamespace>
        <oboInOwl:hasRelatedSynonym>cardiac development</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id>GO:0007507</oboInOwl:id>
        <rdfs:label>heart development</rdfs:label>
    </owl:Class>
@balhoff
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balhoff commented Jan 11, 2025

Thanks @matentzn, I had started working on this then got sidetracked. I will try to get it into the next release.

@balhoff
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balhoff commented Jan 13, 2025

@matentzn I got this merged, so should be out in the next release. Let me know if you would like a sample output.

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2 participants