addresses #17 but massively slows everything down... needs investigation

shapes/go-cam-shapes.shex

@@ -24,6 +24,7 @@ PREFIX GoAnatomicalEntity: <https://purl.obolibrary.org/obo/UBERON_0001062>
 PREFIX GoGrossAnatomicalEntity: <https://purl.obolibrary.org/obo/UBERON_0001062>
 PREFIX GoOrganism: <https://purl.obolibrary.org/obo/NCBITaxon_1>
 PREFIX GoCell: <https://purl.obolibrary.org/obo/CL_0000000>
+PREFIX GoBiologicalPhase: <https://purl.obolibrary.org/obo/GO_0044848>
 #semantic: relations
 PREFIX part_of: <https://purl.obolibrary.org/obo/BFO_0000050>
 PREFIX occurs_in: <https://purl.obolibrary.org/obo/BFO_0000066>
@@ -33,6 +34,19 @@ PREFIX has_output: <https://purl.obolibrary.org/obo/RO_0002234>
 PREFIX directly_provides_input_for: <https://purl.obolibrary.org/obo/RO_0002413>
 PREFIX directly_positively_regulates: <https://purl.obolibrary.org/obo/RO_0002629>
 PREFIX located_in: <https://purl.obolibrary.org/obo/RO_0001025>
+PREFIX happens_during: <https://purl.obolibrary.org/obo/RO_0002092>
+PREFIX regulates: <https://purl.obolibrary.org/obo/RO_0002211>
+PREFIX negatively_regulates: <https://purl.obolibrary.org/obo/RO_0002212>
+PREFIX positively_regulates: <https://purl.obolibrary.org/obo/RO_0002213>
+PREFIX directly_regulates: <https://purl.obolibrary.org/obo/RO_0002578>
+PREFIX directly_negatively_regulates: <https://purl.obolibrary.org/obo/RO_0002630>
+PREFIX directly_positively_regulates: <https://purl.obolibrary.org/obo/RO_0002406>
+PREFIX causally_upstream_of_or_within: <https://purl.obolibrary.org/obo/RO_0002418>
+PREFIX causally_upstream_of_or_within_negative_effect: <https://purl.obolibrary.org/obo/RO_0004046>
+PREFIX causally_upstream_of_or_within_positive_effect: <https://purl.obolibrary.org/obo/RO_0004047>
+PREFIX causally_upstream_of: <https://purl.obolibrary.org/obo/RO_0002411>
+PREFIX causally_upstream_of_negative_effect: <https://purl.obolibrary.org/obo/RO_0002305>
+PREFIX causally_upstream_of_positive_effect: <https://purl.obolibrary.org/obo/RO_0002304>
 
 <GoCamEntity> EXTRA a {
  a [owl:NamedIndividual] {1} // rdfs:comment "Every entity we care about is a named individual";
@@ -61,12 +75,29 @@ PREFIX located_in: <https://purl.obolibrary.org/obo/RO_0001025>
  has_output: @<MolecularEntity> *;
  has_input: @<MolecularEntity> *;
  directly_provides_input_for: @<MolecularFunction> {0,1};
+# happens_during: @<BiologicalPhase> *;
+ regulates: @<MolecularFunction> {0,1};
+ negatively_regulates: @<MolecularFunction> {0,1};
+ positively_regulates: @<MolecularFunction> {0,1};
+ directly_regulates: @<MolecularFunction> {0,1};
+ directly_negatively_regulates: @<MolecularFunction> {0,1};
+ directly_positively_regulates: @<MolecularFunction> {0,1};
+ causally_upstream_of_or_within: @<BiologicalProcess> {0,1};
+ causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> {0,1};
+ causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> {0,1};
+ causally_upstream_of: @<BiologicalProcess> {0,1};
+ causally_upstream_of_negative_effect: @<BiologicalProcess> {0,1};
+ causally_upstream_of_positive_effect: @<BiologicalProcess> {0,1};
 # adding the following seems to break both the js and java shex implementations
 # for: https://noctua-dev.berkeleybop.org/download/gomodel:R-HSA-156582/owl
 # directly_positively_regulates: @<MolecularFunction> *;
 } // rdfs:comment "A molecular function"
 
 
+#<BiologicalPhase> @<GoCamEntity> AND {
+ # bl:category [BiologicalPhase:] ;
+#}// rdfs:comment "an biological phase"
+
 <AnatomicalEntity> @<GoCamEntity> AND {
  bl:category [GoAnatomicalEntity:] ;
 }// rdfs:comment "an anatomical entity"