From 3734d2e0f1d6adee71911c57dc98e989680f8a39 Mon Sep 17 00:00:00 2001
From: vanaukenk <vanauken@caltech.edu>
Date: Fri, 10 May 2024 17:01:49 -0400
Subject: [PATCH] Update go-cam-shapes.shex

Adding  // <exclude_from_extensions> true;
comment to constrain relations' use for standard annotations
---
 shapes/go-cam-shapes.shex | 37 ++++++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 17 deletions(-)

diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex
index dc5684b..82bc851 100644
--- a/shapes/go-cam-shapes.shex
+++ b/shapes/go-cam-shapes.shex
@@ -408,32 +408,32 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <MolecularFunction> @<GoCamEntity> AND EXTRA a {
   a ( @<MolecularFunctionClass> OR @<NegatedMolecularFunctionClass> ) {1};
-  enabled_by:  ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
+  enabled_by:  ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *; // <exclude_from_extensions> true;
   part_of: @<BiologicalProcess> *;
-  has_part: @<MolecularFunction> *;
+  has_part: @<MolecularFunction> *; // <exclude_from_extensions> true;
   occurs_in: @<AnatomicalEntity> {0,1};
   has_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
   has_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
   has_primary_input: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
   has_primary_output: ( @<ChemicalEntity> OR @<ProteinContainingComplex> ) *;
-  directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
+  directly_provides_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true;
   regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
   negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
   positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
   directly_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
   directly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
   directly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
-  indirectly_regulates: ( @<MolecularFunction> OR @<MolecularEvent>) *;
-  indirectly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
-  indirectly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
-  constitutively_upstream_of: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
-  removes_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *;
-  has_small_molecule_regulator: @<ChemicalEntity> *;
-  has_small_molecule_activator: @<ChemicalEntity> *;
-  has_small_molecule_inhibitor: @<ChemicalEntity> *;
-  causally_upstream_of_or_within: ( @<MolecularFunction> OR @<MolecularEvent> OR @<BiologicalProcess> ) *;
-  causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> *;
-  causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> *;
+  indirectly_regulates: ( @<MolecularFunction> OR @<MolecularEvent>) *; // <exclude_from_extensions> true;
+  indirectly_positively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true;
+  indirectly_negatively_regulates: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true;
+  constitutively_upstream_of: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true;
+  removes_input_for: ( @<MolecularFunction> OR @<MolecularEvent> ) *; // <exclude_from_extensions> true;
+  has_small_molecule_regulator: @<ChemicalEntity> *; // <exclude_from_extensions> true;
+  has_small_molecule_activator: @<ChemicalEntity> *; // <exclude_from_extensions> true;
+  has_small_molecule_inhibitor: @<ChemicalEntity> *; // <exclude_from_extensions> true;
+  causally_upstream_of_or_within: ( @<MolecularFunction> OR @<MolecularEvent> OR @<BiologicalProcess> ) *; // <exclude_from_extensions> true;
+  causally_upstream_of_or_within_negative_effect: @<BiologicalProcess> *; // <exclude_from_extensions> true;
+  causally_upstream_of_or_within_positive_effect: @<BiologicalProcess> *; // <exclude_from_extensions> true;
   causally_upstream_of: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
   causally_upstream_of_negative_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
   causally_upstream_of_positive_effect: ( @<BiologicalProcess> OR @<MolecularFunction> OR @<MolecularEvent> ) *;
@@ -524,11 +524,14 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <ProteinContainingComplex> @<GoCamEntity> AND EXTRA a {
   a @<ProteinContainingComplexClass>;
-  located_in: @<AnatomicalEntity> {0,1};
-  is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1};
-  has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex>) *;
+  located_in: @<AnatomicalEntity> {0,1}; // <exclude_from_extensions> true;
+  is_active_in: @<AnatomicalEntity> OR @<RootCellularComponent> {0,1}; // <exclude_from_extensions> true;
+  part_of: @<AnatomicalEntity> {0,1};
+  adjacent_to: @<AnatomicalEntity> *;
+  overlaps: @<AnatomicalEntity> *;
   existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
   existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
+  has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex>) *; // <exclude_from_extensions> true;
 } // rdfs:comment  "a protein complex"
 
 <ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {