infered subject for a certain property value

[gp]

Hello!

I find the new INDIRECT_ prefix to obtain indirect relations very useful and exciting.
From the documentation I understand I cannot perform the inverse where I would query for all subjects which satisfy a certain property value. That is to say, the INDIRECT_ prefix allows me to perform something of the like of the following SPARQL query:

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> 
PREFIX obo: <http://purl.obolibrary.org/obo/> 
PREFIX cl: <http://purl.obolibrary.org/obo/cl.owl>

SELECT distinct ?cellPropValue

WHERE {
graph cl:
    {
       values ?cell {obo:CL_0000928}
       ?cell rdfs:subClassOf* ?cellAncestor .
        
       ?cellAncestor (rdfs:subClassOf|(owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first)) ?x .
       ?x owl:onProperty obo:RO_0002104 ;
          owl:someValuesFrom ?cellPropValue .
      }
}

Limit 100

But I cannot query for something like:

SELECT distinct ?cell ?cellPropValue

WHERE {
    graph cl:
    {   
#        values ?cell {obo:CL_0000928}
       values ?cellPropValue {obo:PR_000001874}
       ?cell (rdfs:subClassOf/(rdfs:subClassOf|(owl:equivalentClass/owl:intersectionOf/rdf:rest*/rdf:first))) ?x .
       ?x owl:onProperty obo:RO_0002104 ;
          owl:someValuesFrom ?cellPropValue .        

    }
}

Limit 100

where these queries are performed against the cell ontology.

Or did I miss something?

Cheers!
GP

[Jiba]

Hello,

For individuals, you can use inverse properties. If the inverse property does not exist, you can create it in a separated temporary ontology, to avoid polluting the main one.

For classes (as your example suggests), it is more complicated. For a formal and logical point of view, one cannot infer restriction on inverse properties from restrictions on a property. For example, "nucleus is part of some cell" does not imply that "cell has part some nucleus": in fact, all cells do not have a nucleus, while all nucleus belong to a cell.

However, it is still interesting in some situations, I agree. Owlready has the Class.inverse_restriction(property) class method that follows restriction in reverse direction. But it does not support indirect relations. Maybe what you would need is a "indirect_inverse_restriction()" method ?

Best regards,
Jiba

[gp]

Hi,

Indeed going for inverse properties makes seldom sense.

In this very case I only want to obtain all cells which are positive for some marker (obo:RO_0002104) and obviously the properties are spread a bit throughout the whole taxonomy, though looking at the parent classes is probably enough in most cases.

The Sparql query I gave does the work (at least partly) but it is notable that it runs very slowly when using the internal rdflib parser. A proper graph server (virtuoso, jena, etc) is able to handle the query in a much more efficient manner (sub-second) so there is some space there.

Thanks for your help and the nice library once again!
GP