[Obo-phenotype] representing EQ annotations in OWL

[Jim B. <ba...@ne...>]

Hi,

I am trying to work with EQ phenotype annotations in Protege and have a question about the best way to model the EQ.  The annotations are at the individual specimen level so I'm trying to figure out which OWL individuals I need to create from the ontology classes.  Given two specimens, "insect1" and "insect2", I have two different ways of describing their head color.  The capitalized terms are OWL classes and come from an anatomy ontology and PATO.

First version - create instances of all terms and link using properties (I assume all instances except for the specimen would be blank nodes when I output this from our database):

<!-- Head instance for this EQ annotation -->
<owl:Thing rdf:about="#_insect1_head">
    <rdf:type rdf:resource="#Head"/>
</owl:Thing>

<!-- Yellow phenotype instance for this EQ annotation -->
<owl:Thing rdf:about="#_insect1_yellow_head">
    <rdf:type rdf:resource="#Yellow"/>
    <inheres_in rdf:resource="#_insect1_head"/>
</owl:Thing>

<!-- Link insect1 to phenotype-->
<owl:Thing rdf:about="#insect1">
       <exhibits rdf:resource="#_insect1_yellow_head"/>
</owl:Thing>


The alternative I thought of is to just create the phenotype individual and declare what it inheres in via its type:

<!-- Red phenotype which inheres_in some Head instance for this EQ annotation -->
<owl:Thing rdf:about="#_insect2_red_head">
    <rdf:type>
        <owl:Class>
            <owl:intersectionOf rdf:parseType="Collection">
                <rdf:Description rdf:about="#Red"/>
                <owl:Restriction>
                    <owl:onProperty rdf:resource="#inheres_in"/>
                    <owl:someValuesFrom rdf:resource="#Head"/>
                </owl:Restriction>
            </owl:intersectionOf>
        </owl:Class>
    </rdf:type>
</owl:Thing>

<!-- Link insect2 to phenotype-->
<owl:Thing rdf:about="#insect2">
       <exhibits rdf:resource="#_insect2_red_head"/>
</owl:Thing>


Is either of these approaches preferred over the other?  Are there any consequences to be aware of?

Thanks,
Jim

____________________________________________
James P. Balhoff, Ph.D.
National Evolutionary Synthesis Center
2024 West Main St., Suite A200
Durham, NC 27705
USA