[Virtuoso-users] Trouble combining OneOrMorePath property path with another graph pattern.

[Todd DeLuca]

I'm trying to combine two graph patterns that each work individually into a
single graph pattern.  However the combined pattern does not have a
solution, even though it should have a solution.  To show what I am doing,
below are several queries which ask: Is there a solution to X?  Is there a
solution to Y?  Is there a solution to X and Y?

In the first set of queries, I use an IRI subject and the ASK queries all
return true, as expected.  In the second set of queries, I use a variable
subject and the ASK query for the combined pattern returns false, even
though we know there is a solution based on the first set of queries.

Am I doing something wrong?  Is there a bug in how the patterns are
matched?  I am using "Virtuoso Open Source Edition (Column Store) (multi
threaded) Version 7.0.0-rc2.3203-pthreads as of Jun 26 2013".

Thanks for any help you can provide.  Here are the queries and their
(true/false) results:

Is human a QfO taxon?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        taxon:9606 dcterms:isPartOf qfo:reference_proteomes-2013_04 .
        }
    " http://localhost:8890/sparql

    true
    real 0m0.046s

Is the human taxon in the primates clade?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        taxon:9606 rdfs:subClassOf+ taxon:9443 .
        }
    " http://localhost:8890/sparql

    true
    real 0m0.043s

Is the human taxon a QfO taxon and in the primates clade?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        taxon:9606 dcterms:isPartOf qfo:reference_proteomes-2013_04 .
        taxon:9606 rdfs:subClassOf+ taxon:9443 .
        }
    " http://localhost:8890/sparql

    true
    real 0m0.392s

Are there taxons that are Qfo taxons?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        ?taxon dcterms:isPartOf qfo:reference_proteomes-2013_04 .
        }
    " http://localhost:8890/sparql

    true
    real 0m0.398s

Are there taxons that are in the primates clade?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        ?taxon rdfs:subClassOf+ taxon:9443 .
        }
    " http://localhost:8890/sparql

    true
    real 0m0.044s

Are there taxons that are QfO taxons and in the primates clade?

    time curl \
    --data-urlencode "query=
        PREFIX qfo:<http://purl.questfororthologs.org/>
        PREFIX dcterms:<http://purl.org/dc/terms/>
        PREFIX obo:<http://purl.org/obo/owl/obo#>
        PREFIX up:<http://purl.uniprot.org/core/>
        PREFIX taxon:<http://purl.uniprot.org/taxonomy/>
        PREFIX rdfs:<http://www.w3.org/2000/01/rdf-schema#>
        PREFIX skos:<http://www.w3.org/2004/02/skos/core#>
        ASK
        WHERE {
        ?taxon dcterms:isPartOf qfo:reference_proteomes-2013_04 .
        ?taxon rdfs:subClassOf+ taxon:9443 .
        }
    " http://localhost:8890/sparql

    false
    real 0m0.408s

Regards,
Todd

-- 
Todd DeLuca
Scientific Programmer
Wall Lab, CBMI, Harvard Medical School
http://todddeluca.com
http://wall.hms.harvard.edu/

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