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information-artifact-ontology / IAO

information artifact ontology
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BFO:0000031 has two definitions causing IAO to not be convertable to OBO via ROBOT #260

Closed StroemPhi closed 1 year ago

StroemPhi commented 2 years ago

In the current IAO release BFO:0000031 has two IAO:0000115 definition axioms (see https://github.com/information-artifact-ontology/IAO/blob/master/iao.owl#L2909-L2910). This causes the conversion to OBO via ROBOT to fail, when using the default settings (see also: http://robot.obolibrary.org/errors#OBO-Structure-Error) This might affect ontologies using IAO downstream that want/need to have an OBO format release.

 <!-- http://purl.obolibrary.org/obo/BFO_0000031 -->

    <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
        <obo:BFO_0000179>gdc</obo:BFO_0000179>
        <obo:BFO_0000180>GenericallyDependentContinuant</obo:BFO_0000180>
        <obo:IAO_0000112 xml:lang="en">The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.</obo:IAO_0000112>
        <obo:IAO_0000112 xml:lang="en">the pdf file on your laptop, the pdf file that is a copy thereof on my laptop</obo:IAO_0000112>
        <obo:IAO_0000112 xml:lang="en">the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.</obo:IAO_0000112>
        <obo:IAO_0000115 xml:lang="en">A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time.</obo:IAO_0000115>
        <obo:IAO_0000115 xml:lang="en">b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])</obo:IAO_0000115>
        <obo:IAO_0000602>(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] </obo:IAO_0000602>
        <rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
        <rdfs:label xml:lang="en">generically dependent continuant</rdfs:label>
    </owl:Class>
alanruttenberg commented 2 years ago

FWIW Here is what the ISO version has. A.1.2.50 generically dependent continuant SYNONYM: g-dependent continuant ELUCIDATION: a generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies; it is the content or the pattern that the multiple copies share EXAMPLES: The pdf file on your laptop, the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint.

zhengj2007 commented 2 years ago

IAO imported both BFO and RO core OWL files, which contain different definitions of BFO:0000031. I will clean up the definition manually on the coming release.