Reactome test: standard and sygenia queries.

3 files changed, 932 insertions, 0 deletions

diff --git a/data/reactome/reactome_sygenia_queries.sparql b/data/reactome/reactome_sygenia_queries.sparql
new file mode 100644
index 0000000..97ba1c9
--- /dev/null
+++ b/data/reactome/reactome_sygenia_queries.sparql
@@ -0,0 +1,649 @@
+^[query1]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:CellVocabulary 
+}
+
+^[query2]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:cofactor _:y 
+}
+
+^[query3]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:participant _:y .
+  _:y rdf:type reactome:PhysicalEntity 
+}
+
+^[query4]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SequenceRegionVocabulary 
+}
+
+^[query5]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x ?y
+WHERE {
+  ?x reactome:bindsTo ?y 
+}
+
+^[query6]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:EntityFeature 
+}
+
+^[query7]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Score 
+}
+
+^[query8]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:ExperimentalForm 
+}
+
+^[query9]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepProcess _:y .
+  _:y rdf:type reactome:Conversion 
+}
+
+^[query10]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepProcess _:y .
+  _:y rdf:type reactome:Entity 
+}
+
+^[query11]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:PathwayStep 
+}
+
+^[query12]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:RelationshipTypeVocabulary 
+}
+
+^[query13]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:TissueVocabulary 
+}
+
+^[query14]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  _:y reactome:bindsTo ?x 
+}
+
+^[query15]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepConversion _:y 
+}
+
+^[query16]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Conversion 
+}
+
+^[query17]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Control 
+}
+
+^[query18]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Catalysis 
+}
+
+^[query19]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepConversion _:y .
+  _:y rdf:type reactome:Conversion 
+}
+
+^[query20]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:right _:y .
+  _:y rdf:type reactome:Entity 
+}
+
+^[query21]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x ?y
+WHERE {
+  ?x reactome:participant ?y 
+}
+
+^[query22]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:left _:y 
+}
+
+^[query23]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:product _:y 
+}
+
+^[query24]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:PhenotypeVocabulary 
+}
+
+^[query25]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepProcess _:y 
+}
+
+^[query26]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  _:y reactome:bindsTo ?x .
+  _:y rdf:type reactome:EntityFeature 
+}
+
+^[query27]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:cofactor _:y .
+  _:y rdf:type reactome:PhysicalEntity 
+}
+
+^[query28]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x ?y
+WHERE {
+  ?x reactome:stepProcess ?y 
+}
+
+^[query29]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Stoichiometry 
+}
+
+^[query30]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:UtilityClass 
+}
+
+^[query31]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:ChemicalStructure 
+}
+
+^[query32]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SequenceSite 
+}
+
+^[query33]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:BioSource 
+}
+
+^[query34]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  _:y reactome:bindsTo ?x .
+  _:y rdf:type reactome:UtilityClass 
+}
+
+^[query35]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:ControlledVocabulary 
+}
+
+^[query36]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Transport 
+}
+
+^[query37]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:bindsTo _:y 
+}
+
+^[query38]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:template _:y 
+}
+
+^[query39]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:participant _:y 
+}
+
+^[query40]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:controlled _:y 
+}
+
+^[query41]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:ModificationFeature 
+}
+
+^[query42]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x ?y
+WHERE {
+  ?y reactome:bindsTo ?x 
+}
+
+^[query43]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:InteractionVocabulary 
+}
+
+^[query44]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SequenceModificationVocabulary 
+}
+
+^[query45]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:right _:y .
+  _:y rdf:type reactome:PhysicalEntity 
+}
+
+^[query46]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:participant _:y .
+  _:y rdf:type reactome:Entity 
+}
+
+^[query47]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:EvidenceCodeVocabulary 
+}
+
+^[query48]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Complex 
+}
+
+^[query49]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Provenance 
+}
+
+^[query50]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SequenceLocation 
+}
+
+^[query51]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:right _:y 
+}
+
+^[query52]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Evidence 
+}
+
+^[query53]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:TemplateReaction 
+}
+
+^[query54]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Entity 
+}
+
+^[query55]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:bindsTo _:y .
+  _:y rdf:type reactome:BindingFeature 
+}
+
+^[query56]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Xref 
+}
+
+^[query57]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:BiochemicalReaction 
+}
+
+^[query58]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:stepProcess _:y .
+  _:y rdf:type reactome:Interaction 
+}
+
+^[query59]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:BindingFeature 
+}
+
+^[query60]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:RelationshipXref 
+}
+
+^[query61]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:PhysicalEntity 
+}
+
+^[query62]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:CellularLocationVocabulary 
+}
+
+^[query63]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:EntityReference 
+}
+
+^[query64]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:bindsTo _:y .
+  _:y rdf:type reactome:UtilityClass 
+}
+
+^[query65]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:left _:y .
+  _:y rdf:type reactome:Entity 
+}
+
+^[query66]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:KPrime 
+}
+
+^[query67]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:GeneticInteraction 
+}
+
+^[query68]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:bindsTo _:y .
+  _:y rdf:type reactome:EntityFeature 
+}
+
+^[query69]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Interaction 
+}
+
+^[query70]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:ExperimentalFormVocabulary 
+}
+
+^[query71]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:left _:y .
+  _:y rdf:type reactome:PhysicalEntity 
+}
+
+^[query72]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SequenceInterval 
+}
+
+^[query73]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:BiochemicalPathwayStep 
+}
+
+^[query74]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:Pathway 
+}
+
+^[query75]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x reactome:controller _:y 
+}
+
+^[query76]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  _:y reactome:bindsTo ?x .
+  _:y rdf:type reactome:BindingFeature 
+}
+
+^[query77]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:SmallMoleculeReference 
+}
+
+^[query78]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:DeltaG 
+}
+
+^[query79]
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX reactome: <http://www.biopax.org/release/biopax-level3.owl#>
+SELECT ?x
+WHERE {
+  ?x rdf:type reactome:EntityReferenceTypeVocabulary 
+}
+
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java b/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
new file mode 100644
index 0000000..2fc682b
--- /dev/null
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/SkolemisationTests.java
@@ -0,0 +1,269 @@
+package uk.ac.ox.cs.pagoda.global_tests;
+
+import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.model.*;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+import uk.ac.ox.cs.pagoda.query.AnswerTuple;
+import uk.ac.ox.cs.pagoda.query.AnswerTuples;
+import uk.ac.ox.cs.pagoda.query.QueryRecord;
+import uk.ac.ox.cs.pagoda.reasoner.QueryReasoner;
+import uk.ac.ox.cs.pagoda.util.TestUtil;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+
+public class SkolemisationTests {
+
+    public static final String NS = "http://example.org/test#%s";
+
+    private IRI getEntityIRI(String name) {
+        return IRI.create(String.format(NS, name));
+    }
+
+//    @Test
+    public void commonSuccessorTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, c));    // A(c)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, d));    // A(d)
+
+        // Minimum cardinality axiom
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectUnionOf(
+                                                               factory.getOWLObjectSomeValuesFrom(roleR, classB),
+                                                               factory.getOWLObjectSomeValuesFrom(roleR, classC))));
+
+        /*
+         * Save the ontology
+         * */
+
+//        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "select distinct ?x ?y " +
+                    " where { "
+                    + " ?x <" + roleR.toStringID() + "> _:z . "
+                    + " ?y <" + roleR.toStringID() + "> _:z " +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+            Assert.assertEquals(count, 2);
+        }
+        pagoda.dispose();
+    }
+
+//    @Test
+    public void yTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+        OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+        OWLObjectProperty roleS = factory.getOWLObjectProperty(IRI.create(String.format(NS, "S")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleS));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, a));    // D(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classD, b));    // D(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleS, c, a)); // S(c,a)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, d, b)); // P(d,b)
+
+        // Axioms
+        // subsetOf(D someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classD,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+        // subsetOf(someValuesFrom(inverseOf(S) owl:Thing) allValuesFrom(R A))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleS.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       factory.getOWLObjectAllValuesFrom(roleR, classA)));
+        // subsetOf(someValuesFrom(inverseOf(P) owl:Thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        // subsetOf(someValuesFrom(R A) C)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleR, classA), classC));
+
+        /*
+         * Save the ontology
+         * */
+
+        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+//                    + " ?x rdf:type " + classB + " ."
+//                    + " ?x " + roleR + " "+ "_:y . "
+                    + " ?x rdf:type " + classC +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+//            Assert.assertEquals(count, 1);
+        }
+        pagoda.dispose();
+    }
+
+    @Test
+    public void rTest() throws OWLOntologyCreationException, IOException, OWLOntologyStorageException {
+
+        /*
+         * Build test ontology
+         * */
+
+        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
+        OWLDataFactory factory = manager.getOWLDataFactory();
+        OWLOntology ontology = manager.createOntology();
+
+        OWLClass classA = factory.getOWLClass(getEntityIRI("A"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classA));
+        OWLClass classB = factory.getOWLClass(getEntityIRI("B"));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classB));
+//        OWLClass classC = factory.getOWLClass(getEntityIRI("C"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classC));
+//        OWLClass classD = factory.getOWLClass(getEntityIRI("D"));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(classD));
+        OWLNamedIndividual a = factory.getOWLNamedIndividual(getEntityIRI("a"));
+        OWLNamedIndividual b = factory.getOWLNamedIndividual(getEntityIRI("b"));
+        OWLNamedIndividual c = factory.getOWLNamedIndividual(getEntityIRI("c"));
+//        OWLNamedIndividual d = factory.getOWLNamedIndividual(getEntityIRI("d"));
+        OWLObjectProperty roleR = factory.getOWLObjectProperty(IRI.create(String.format(NS, "R")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleR));
+//        OWLObjectProperty roleF = factory.getOWLObjectProperty(IRI.create(String.format(NS, "F")));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleF));
+        OWLObjectProperty roleP = factory.getOWLObjectProperty(IRI.create(String.format(NS, "P")));
+        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleP));
+//        OWLObjectProperty roleL = factory.getOWLObjectProperty(IRI.create(String.format(NS, "L")));
+//        manager.addAxiom(ontology, factory.getOWLDeclarationAxiom(roleL));
+
+        // Class assertions
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, a));    // A(a)
+        manager.addAxiom(ontology, factory.getOWLClassAssertionAxiom(classA, b));    // A(b)
+        manager.addAxiom(ontology, factory.getOWLObjectPropertyAssertionAxiom(roleP, c, a)); // P(c,a)
+
+        // Axioms
+        // subsetOf(A someValuesFrom(R owl:Thing))
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(classA,
+                                                       factory.getOWLObjectSomeValuesFrom(roleR,
+                                                                                          factory.getOWLThing())));
+
+        // inverseFunctional(R)
+        manager.addAxiom(ontology,
+                         factory.getOWLInverseFunctionalObjectPropertyAxiom(roleR));
+
+        // subsetOf(someValuesFrom(inverseOf(P) owl:thing) B)
+        manager.addAxiom(ontology,
+                         factory.getOWLSubClassOfAxiom(factory.getOWLObjectSomeValuesFrom(roleP.getInverseProperty(),
+                                                                                          factory.getOWLThing()),
+                                                       classB));
+        /*
+         * Save the ontology
+         * */
+
+        manager.saveOntology(ontology, Files.newOutputStream(Paths.get("/home/alessandro/Desktop/test-ontology.owl")));
+
+        /*
+         * Test one query
+         * */
+
+        QueryReasoner pagoda = QueryReasoner.getInstance(ontology);
+        pagoda.loadOntology(ontology);
+        if(pagoda.preprocess()) {
+            String queryStr = "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> " +
+                    "select distinct ?x" +
+                    " where { "
+                    + " ?x rdf:type " + classB +
+                    " }";
+            QueryRecord queryRecord = pagoda.getQueryManager().create(queryStr);
+            System.out.println(queryRecord);
+            pagoda.evaluate(queryRecord);
+            AnswerTuples answers = queryRecord.getAnswers();
+            System.out.println("Difficulty: " + queryRecord.getDifficulty());
+            int count = 0;
+            for(AnswerTuple ans; answers.isValid(); answers.moveNext()) {
+                ans = answers.getTuple();
+                TestUtil.logInfo(ans);
+                count++;
+            }
+//            Assert.assertEquals(count, 1);
+        }
+        pagoda.dispose();
+    }
+}
diff --git a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
index 5c05b94..30f3d93 100644
--- a/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
+++ b/test/uk/ac/ox/cs/pagoda/global_tests/TestPagodaReactome.java
@@ -23,4 +23,18 @@ public class TestPagodaReactome {
               .run();
     }
 
+    @Test(groups = {"sygenia"})
+    public void justExecute_sygenia() throws IOException {
+        String ontoDir = TestUtil.getConfig().getProperty("ontoDir");
+
+        Pagoda.builder()
+              .ontology(Paths.get(ontoDir, "reactome/biopax-level3-processed.owl"))
+              .data(Paths.get(ontoDir, "reactome/data/sample_10.ttl"))
+              .query(Paths.get(ontoDir, "reactome/reactome_sygenia_queries.sparql"))
+              .classify(true)
+              .hermit(true)
+              .build()
+              .run();
+    }
+
 }