Select single class and all of its properties as a subset

[davidshumway]

Is there a method in rdflib to extract a single class and all of its associated properties, for example, if one had a list of classes they wanted to add to another ontology (i.e. Graph())?

For example, consider the following class from IDO: http://purl.obolibrary.org/obo/IDO_0000406 (see below). In this example, it might be easier to simply parse the contents of the ontology's OWL file using a regex pattern such as /(<owl:Class .+?\s\s\s\s\n<\/owl:Class>/ to capture all of the classes, after which the classes of interest could simply be filtered out and appended to a new OWL file.

Loading the ontology as a new Graph() and iterating through all of the statements seems like a tough way to go because e.g. in this case there are a number of <owl:Restriction>, <owl:intersectionOf>, etc. statements which end up as anonymous classes.

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_0000406">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IDO_0000452"/>
        <rdfs:subClassOf>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/OBI_0100026"/>
                    </owl:Restriction>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
                        <owl:allValuesFrom>
                            <owl:Class>
                                <owl:intersectionOf rdf:parseType="Collection">
                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
                                    <owl:Restriction>
                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IDO_0000625"/>
                                    </owl:Restriction>
                                    <owl:Restriction>
                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
                                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/TRANS_0000000"/>
                                    </owl:Restriction>
                                    <owl:Restriction>
                                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
                                        <owl:someValuesFrom>
                                            <owl:Class>
                                                <owl:intersectionOf rdf:parseType="Collection">
                                                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/IDO_0000626"/>
                                                    <owl:Class>
                                                        <owl:complementOf>
                                                            <owl:Restriction>
                                                                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000066"/>
                                                                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/IDO_0000457"/>
                                                            </owl:Restriction>
                                                        </owl:complementOf>
                                                    </owl:Class>
                                                </owl:intersectionOf>
                                            </owl:Class>
                                        </owl:someValuesFrom>
                                    </owl:Restriction>
                                </owl:intersectionOf>
                            </owl:Class>
                        </owl:allValuesFrom>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </rdfs:subClassOf>
        <obo:IAO_0000115 xml:lang="en">An infectious disposition to become part of a disorder only in organisms whose defenses are compromised.</obo:IAO_0000115>
        <obo:IAO_0000117>Albert Goldfain</obo:IAO_0000117>
        <obo:IAO_0000117>Alexander Diehl</obo:IAO_0000117>
        <obo:IAO_0000117>Lindsay Cowell</obo:IAO_0000117>
        <obo:IAO_0000118 xml:lang="en">opportunitistic pathogenic disposition</obo:IAO_0000118>
        <rdfs:comment>The disposition is realized in a process by which the bearer becomes part of a disorder in an immunocompromised host.</rdfs:comment>
        <rdfs:comment xml:lang="en">This includes individuals who are immunocompromised or who have damaged barriers that normally protect against infection (e.g. skin).</rdfs:comment>
        <rdfs:label xml:lang="en">opportunistic infectious disposition</rdfs:label>
    </owl:Class>

[aucampia]

@davidshumway it is a bit unclear what exactly you want, but possibly you could use rdflib.Graph.triples

g.triples((None, RDF.type, URIRef(http://purl.obolibrary.org/obo/IDO_0000406)))

If you can provide a complete graph, and exact results you want, it would be easier.

[davidshumway]

Thanks, @aucampia. An example graph would be IDO: https://ontobee.org/ontology/IDO. The issue that I faced with iterating using triples(...) is that there are anonymous classes picked up by rdflib due to OWL syntax.

For now, I used this tool to extract the classes and associated axioms of interest: (http://robot.obolibrary.org/extract).

[davidshumway]

So for example from the excerpt above for IDO_0000406: <rdfs:subClassOf> <owl:Class> <owl:intersectionOf rdf:parseType="Collection"> ... </owl:intersectionOf> </owl:Class> </rdfs:subClassOf>. As a triple, this comes out as IDO_0000406->rdfs:subClassOf-> [N.....] where N.... is an anonymous entity representing the <owl:Class> element. Then N.... has another triple connecting to the <owl:intersectionOf...> element. The intersection element itself is another anonymous entity. So it's apparent that there quickly is no further reference to the original class IDO_0000406 in these triples. So that's where iterating through the triples appears to fail to capture all of the "insides" of IDO_0000406. Perhaps I'm missing something?

[davidshumway]

Iterating through triples(...) is only going to return first-level connections to IDO_0000406. There would have to be a recursive call in here to "drill down" into the anonymous entities if they are going to be included.