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Link to original content: http://github.com/EBISPOT/DUO/issues/123
DUO:0000015 missing datatype for shorthand · Issue #123 · EBISPOT/DUO · GitHub
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DUO:0000015 missing datatype for shorthand #123

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amstilp opened this issue Dec 28, 2022 · 0 comments
Open

DUO:0000015 missing datatype for shorthand #123

amstilp opened this issue Dec 28, 2022 · 0 comments

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@amstilp
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amstilp commented Dec 28, 2022

I'm not very familiar with owl files, so apologies if I'm using any vocabulary incorrectly here. I'm also not sure if this issue is more appropriate in this repo vs in the pronto repo (https://github.com/althonos/pronto).

The definition of DUO:0000015 appears to be missing the datatype for "shorthand":

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000015">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000017"/>
        <obo:IAO_0000115 xml:lang="en">This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).</obo:IAO_0000115>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000015</oboInOwl:id>
        <oboInOwl:shorthand>NMDS</oboInOwl:shorthand>
        <rdfs:label xml:lang="en">no general methods research</rdfs:label>
    </owl:Class>

Other terms have the datatype specified in the oboInOwl:shorthand tag, for example:

<oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GRU</oboInOwl:shorthand>

If I try to parse duo-basic.owl or duo.owl using pronto, the shorthand is not listed as an annotation:

>>> from pronto import Ontology
>>> duo = Ontology("https://raw.githubusercontent.com/EBISPOT/DUO/master/duo-basic.owl")
>>> duo["DUO:0000042"].annotations
{LiteralPropertyValue('http://www.geneontology.org/formats/oboInOwl#shorthand', 'GRU')}
>>> duo["DUO:0000015"].annotations
set()

This breaks automated processing that I'm trying to do for the duo.owl files. Using pronto, the shorthand is not listed as an annotation.

If I change the definition of DUO:0000015 to

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/DUO_0000015">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/DUO_0000017"/>
        <obo:IAO_0000115 xml:lang="en">This data use modifier indicates that use does not allow methods development research (e.g., development of software or algorithms).</obo:IAO_0000115>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">DUO:0000015</oboInOwl:id>
        <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">NMDS</oboInOwl:shorthand>
        <rdfs:label xml:lang="en">no general methods research</rdfs:label>
    </owl:Class>

then pronto does find the annotations/shorthand for DUO:0000015.
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