./d2r-query --verbose mapping_pubchem.ttl @q10.sparql
00:48:14 INFO  SystemLoader         :: Reading mapping file FROM mapping_pubchem.ttl
00:48:14 INFO  MapParser            :: Done reading D2RQ map WITH 1 DATABASES AND 118 class maps
00:48:14 INFO  d2r_query            :: Query:
PREFIX : <http://annotation.semanticweb.org/iswc/iswc.daml#>
PREFIX template: <http://bioinfo.iocb.cz/0.9/template#>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX iswc: <http://annotation.semanticweb.org/iswc/iswc.daml#>
PREFIX concept: <http://rdf.ncbi.nlm.nih.gov/pubchem/concept/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX obov: <http://purl.obolibrary.org/obo#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bp: <http://www.biopax.org/release/biopax-level3.owl#>
PREFIX cito: <http://purl.org/spar/cito/>
PREFIX bao: <http://www.bioassayontology.org/bao#>
PREFIX protein: <http://rdf.ncbi.nlm.nih.gov/pubchem/protein/>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX vocab: <http://rdf.ncbi.nlm.nih.gov/pubchem/vocabulary#>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX map: <http://example.com/test/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX proc: <http://bioinfo.iocb.cz/rdf/0.9/procedure-calls#>
PREFIX fabio: <http://purl.org/spar/fabio/>
PREFIX substance: <http://rdf.ncbi.nlm.nih.gov/pubchem/substance/>
PREFIX conserveddomain: <http://rdf.ncbi.nlm.nih.gov/pubchem/conserveddomain/>
PREFIX vcard: <http://www.w3.org/2001/vcard-rdf/3.0#>
PREFIX compound: <http://rdf.ncbi.nlm.nih.gov/pubchem/compound/>
PREFIX orchem: <http://bioinfo.iocb.cz/0.9/orchem#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX pdbo: <http://rdf.wwpdb.org/schema/pdbx-v40.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX dc: <http://purl.org/dc/elements/1.1/>
SELECT (COUNT(?sub) AS ?subcnt) ?protein
    WHERE {
        ?sub obo:BFO_0000056 ?mg .
        ?mg obo:BFO_0000057 ?protein .
        ?protein rdf:TYPE bp:Protein .
        ?mg obo:OBI_0000299 ?ep .
        ?ep rdf:TYPE bao:BAO_0000190 ; obo:IAO_0000136 ?sub ; sio:has-VALUE ?VALUE .
    }
    GROUP BY ?protein
    ORDER BY DESC (COUNT(?sub))
00:48:15 INFO  ConnectedDB          :: Establishing JDBC connection TO jdbc:postgresql://localhost:5432/rdf
00:48:15 INFO  ConnectedDB          :: JDBC DATABASE product TYPE: PostgreSQL
00:48:15 INFO  ConnectedDB          :: USING vendor class: de.fuberlin.wiwiss.d2rq.SQL.vendor.PostgreSQL
00:48:15 INFO  Mapping              :: Compiled 203 property bridges
00:48:15 INFO  SQLIterator          :: SELECT DISTINCT "T7_endpoint_merged"."value", "T4_endpoint_merged"."substance", "T4_endpoint_merged"."measuregroup", "T6_endpoint_merged"."substance", "T2_protein_bases"."name", "T4_endpoint_merged"."bioassay" FROM "protein_bases" AS "T3_protein_bases", "endpoint_merged" AS "T1_endpoint_merged", "endpoint_merged" AS "T5_endpoint_merged", "endpoint_merged" AS "T4_endpoint_merged", "measuregroup_proteins" AS "T2_measuregroup_proteins", "protein_bases" AS "T2_protein_bases", "endpoint_merged" AS "T7_endpoint_merged", "endpoint_merged" AS "T6_endpoint_merged" WHERE ("T1_endpoint_merged"."bioassay" = "T2_measuregroup_proteins"."bioassay" AND "T1_endpoint_merged"."measuregroup" = "T2_measuregroup_proteins"."measuregroup" AND "T1_endpoint_merged"."substance" = "T6_endpoint_merged"."substance" AND "T2_measuregroup_proteins"."bioassay" = "T4_endpoint_merged"."bioassay" AND "T2_measuregroup_proteins"."measuregroup" = "T4_endpoint_merged"."measuregroup" AND "T2_protein_bases"."name" = "T3_protein_bases"."name" AND "T4_endpoint_merged"."bioassay" = "T5_endpoint_merged"."bioassay" AND "T4_endpoint_merged"."measuregroup" = "T5_endpoint_merged"."measuregroup" AND "T4_endpoint_merged"."substance" = "T5_endpoint_merged"."substance" AND "T5_endpoint_merged"."bioassay" = "T6_endpoint_merged"."bioassay" AND "T5_endpoint_merged"."bioassay" = "T7_endpoint_merged"."bioassay" AND "T5_endpoint_merged"."measuregroup" = "T6_endpoint_merged"."measuregroup" AND "T5_endpoint_merged"."measuregroup" = "T7_endpoint_merged"."measuregroup" AND "T5_endpoint_merged"."substance" = "T6_endpoint_merged"."substance" AND "T5_endpoint_merged"."substance" = "T7_endpoint_merged"."substance" AND "T5_endpoint_merged"."type" = 190 AND "T5_endpoint_merged"."type" IS NOT NULL AND "T7_endpoint_merged"."value" IS NOT NULL AND ("T2_measuregroup_proteins"."protein"="T2_protein_bases"."id") AND ("T7_endpoint_merged"."value" IS NOT NULL))