Select single ontology class and all of its axioms and annotations as a subset

Question

Is there a SPARQL or other method to extract a single class and all of its associated axioms and annotations from an ontology? For example, assume one had a list of classes from one ontology that they wanted to add to another ontology.

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\s\n<\/owl:Class>/ to capture all of the details of every class after which the classes of interest could simply be filtered out and appended to a new OWL file.

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IDO_...">
    ...
</owl:Class>

...

<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>

EDIT: I tried using rdflib to achieve this by loading the source ontology as a Graph(). Using a for loop to iterate through statements in the loaded graph, it's easy enough to find the triples which are directly connected to a class, say, ido:IDO_0000406 -> obo:IAO_0000117 -> Alexander Diehl. These can then be added to the target ontology, which is also loaded as a graph. However, using the IDO_0000406 class example, it is clear that triples not on the first sub-level (i.e. anything within the clause <rdfs:subClassOf><owl:Class>...) will not come through as expected. For example:

g_tgt = Graph()
classes = ['http://purl.obolibrary.org/obo/IDO_0000406'
  'http://purl.obolibrary.org/obo/IDO_0000407',
  'http://purl.obolibrary.org/obo/IDO_0000408',
  'http://purl.obolibrary.org/obo/IDO_0000409']

g_src = Graph()
g_src.parse('ido.owl')
for stmt in g_src: # stmt: (subject, predicate, object)
  if str(stmt[0]) in classes:
    # adds all first-level triples to target graph
    g_tgt.add((stmt[0], stmt[1], stmt[2]))

My thought is to approach non-first-level nodes in a recursive fashion and will update if this is successful.

EDIT 2: It should be possible to extract the classes using ROBOT (http://robot.obolibrary.org/extract). For example:

robot extract --method STAR \
    --input filtered.owl \
    --term-file uberon_module.txt \
    --output results/uberon_module.owl

where uberon_module.txt would include the list of classes to be extracted.

the easiest way is to use a proper OWL library to parse and process the ontology. With SPARQL it's for obvious reason more difficult up to impossible as it's made for RDF. Even if you'd get back the corresponding RDF triples making OWL axioms and possible complex class expressions like in your example, you need something that would be able to parse it. — UninformedUser, Sep 04 '22 at 19:00
@UninformedUser I tried using rdflib to achieve this by loading the source ontology as a `Graph()`. Using a for loop to iterate through statements in the loaded graph, it's easy enough to find the triples which are directly connected to a class, say, `ido:IDO_0000406 -> obo:IAO_0000117 -> Alexander Diehl`. And then add these to my target ontology, also loaded as a graph. However, from the example in my question, it is clear that the triples not on the first sub-level (e.g. anything within the clause `...`) will not come through clearly. — There, Sep 04 '22 at 20:31
It would seem a SPARQL `DESCRIBE` query could achieve what you want. Depending on the endpoint, it could return the triples describing the class or any blank nodes that are encountered, which seems to be what is within the `` in your example. — IS4, Sep 05 '22 at 08:58

Select single ontology class and all of its axioms and annotations as a subset

0 Answers0