diff --git a/README.md b/README.md
index 39878ac..c50af18 100644
--- a/README.md
+++ b/README.md
@@ -4,7 +4,6 @@
 
 Using RDF Shapes to define the schema of Gene Ontology Causal Activity Models
 
-
 # Schema
 
 See [shapes/go-cam-shapes.shex](shapes/go-cam-shapes.shex)
diff --git a/shapes/WIP_standard_annot_ShEx b/shapes/WIP_standard_annot_ShEx
index 2439c83..1ec1503 100644
--- a/shapes/WIP_standard_annot_ShEx
+++ b/shapes/WIP_standard_annot_ShEx
@@ -172,6 +172,8 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   part_of: @<BiologicalProcess> *;
   has_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
   has_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
+  has_primary_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
+  has_primary_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
   occurs_in: @<AnatomicalEntity> {0,1};
   has_target_end_location: @<AnatomicalEntity> {0,1};
   has_target_start_location: @<AnatomicalEntity> {0,1};
@@ -457,18 +459,18 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 <ProteinContainingComplex> @<GoCamEntity> AND EXTRA a {
   a @<ProteinContainingComplexClass>;
   enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
-  contributes_to: @<MolecularFunction> {0,1};
   located_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> ) {0,1};
   is_active_in: ( @<CellularAnatomicalEntity> OR @<RootCellularComponent> OR @VirionComponent> ) {0,1};
   part_of: @<ProteinContainingComplex> *;
-  has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
-  existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
-  existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
   involved_in: ( @<BiologicalProcess> OR @<RootBiologicalProcess> ) {0,1}; 
   acts_upstream_of_negative_effect: @<BiologicalProcess> {0,1};
   acts_upstream_of_positive_effect: @<BiologicalProcess> {0,1};
   acts_upstream_of_or_within_negative_effect: @<BiologicalProcess> {0,1};
-  acts_upstream_of_or_within_positive_effect: @<BiologicalProcess> {0,1};	
+  acts_upstream_of_or_within_positive_effect: @<BiologicalProcess> {0,1};
+  has_part: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
+  existence_overlaps: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
+  existence_starts_and_ends_during: ( @<BiologicalProcess> OR @<LifeCycleStage> OR @<PlantStructureDevelopmentStage> ) *;
+  
 } // rdfs:comment  "a protein complex"
 
 <ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex
index 47201c5..e9690ec 100644
--- a/shapes/go-cam-shapes.shex
+++ b/shapes/go-cam-shapes.shex
@@ -129,6 +129,7 @@ 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>
 
+
 <GoCamModel> {
   a [owl:Ontology] + ;
   contributor: xsd:string +; #TODO would be better as an IRI
@@ -193,6 +194,8 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   part_of: @<BiologicalProcess> *;
   has_input: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> OR @<Organism> ) *;
   has_output: ( @<ChemicalEntity> OR @<AnatomicalEntity> OR @<ProteinContainingComplex> ) *;
+  has_primary_input: @<ChemicalEntity> *;
+  has_primary_output: @<ChemicalEntity> *;
   occurs_in: @<AnatomicalEntity> {0,1};
   transports_or_maintains_localization_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) *;
   has_target_end_location: @<AnatomicalEntity> {0,1};
@@ -405,32 +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> ) *;
@@ -521,11 +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 {