Add GP-to-BP relations, and handle negated GO terms with extensions.

geneontology · Jan 30, 2024 · 3903c47 · 3903c47
1 parent 5c07037
commit 3903c47
Showing 1 changed file with 24 additions and 3 deletions.
diff --git a/shapes/gpad-shapes.shex b/shapes/gpad-shapes.shex
@@ -131,6 +131,13 @@ PREFIX results_in_maturation_of: <http://purl.obolibrary.org/obo/RO_0002299>
 PREFIX results_in_growth_of: <http://purl.obolibrary.org/obo/RO_0002343>
 PREFIX results_in_movement_of: <http://purl.obolibrary.org/obo/RO_0002565>
 PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
+PREFIX acts_upstream_of: <http://purl.obolibrary.org/obo/RO_0002263>
+PREFIX acts_upstream_of_positive_effect: <http://purl.obolibrary.org/obo/RO_0004034>
+PREFIX acts_upstream_of_negative_effect: <http://purl.obolibrary.org/obo/RO_0004035>
+PREFIX acts_upstream_of_or_within: <http://purl.obolibrary.org/obo/RO_0002264>
+PREFIX acts_upstream_of_or_within_positive_effect: <http://purl.obolibrary.org/obo/RO_0004032>
+PREFIX acts_upstream_of_or_within_negative_effect: <http://purl.obolibrary.org/obo/RO_0004033>
+PREFIX involved_in: <http://purl.obolibrary.org/obo/RO_0002331>
 
 <GoCamModel> {
   a [owl:Ontology] + ;
@@ -181,7 +188,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <GOTermInstance> IRI {
   a [ owl:NamedIndividual ] ;
-  a [ GO:~ ]
+  a ( [ GO:~ ] OR ( BNode AND ( { owl:complementOf [ GO:~ ] } ) ) )
 }
 
 <ExtensionNode> IRI CLOSED {
@@ -211,7 +218,14 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
     ^causally_upstream_of_negative_effect: @<MolecularFunction> |
     ^causally_upstream_of_or_within: @<MolecularFunction> |
     ^causally_upstream_of_or_within_positive_effect: @<MolecularFunction> |
-    ^causally_upstream_of_or_within_negative_effect: @<MolecularFunction>
+    ^causally_upstream_of_or_within_negative_effect: @<MolecularFunction> |
+    ^acts_upstream_of: @<DBObject> |
+    ^acts_upstream_of_positive_effect: @<DBObject> |
+    ^acts_upstream_of_negative_effect: @<DBObject> |
+    ^acts_upstream_of_or_within: @<DBObject> |
+    ^acts_upstream_of_or_within_positive_effect: @<DBObject> |
+    ^acts_upstream_of_or_within_negative_effect: @<DBObject> |
+    ^involved_in: @<DBObject>
   ) ;
   occurs_in: @<CellularComponent> {0,1};
 } // rdfs:comment  "A biological process instance"
@@ -286,7 +300,14 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
     is_active_in: @<CellularComponent> |
     colocalizes_with: @<CellularComponent> |
     ^enabled_by: @<MolecularFunction> |
-    contributes_to: @<MolecularFunction>
+    contributes_to: @<MolecularFunction> |
+    acts_upstream_of: @<BiologicalProcess> |
+    acts_upstream_of_positive_effect: @<BiologicalProcess> |
+    acts_upstream_of_negative_effect: @<BiologicalProcess> |
+    acts_upstream_of_or_within: @<BiologicalProcess> |
+    acts_upstream_of_or_within_positive_effect: @<BiologicalProcess> |
+    acts_upstream_of_or_within_negative_effect: @<BiologicalProcess> |
+    involved_in: @<BiologicalProcess>
   )
 }