From c289f9ac401ab832046c7826ec09f4110c959c88 Mon Sep 17 00:00:00 2001
From: vanaukenk <vanauken@caltech.edu>
Date: Tue, 19 Mar 2024 12:26:05 -0400
Subject: [PATCH] Update WIP_standard_annot_ShEx

---
 shapes/WIP_standard_annot_ShEx | 46 +++++++++++++++++-----------------
 1 file changed, 23 insertions(+), 23 deletions(-)

diff --git a/shapes/WIP_standard_annot_ShEx b/shapes/WIP_standard_annot_ShEx
index dcfcfed..2439c83 100644
--- a/shapes/WIP_standard_annot_ShEx
+++ b/shapes/WIP_standard_annot_ShEx
@@ -456,19 +456,19 @@ 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};
+  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> *;
+  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};	
+  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};	
 } // rdfs:comment  "a protein complex"
 
 <ProteinContainingComplexClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -480,33 +480,33 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 }
 <Protein> @<ChemicalEntity> AND EXTRA a {
   a @<ProteinClass> ;
-	enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
-	contributes_to: @<MolecularFunction> {0,1};
+  enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
+  contributes_to: @<MolecularFunction> {0,1};
   located_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> ) {0,1};
   is_active_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> OR @<RootCellularComponent> ) {0,1};
   part_of: @<ProteinContainingComplex> {0,1};
-	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};	
+  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};	
 }// rdfs:comment  "a protein"
 
 <InformationBiomacromoleculeClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
   rdfs:subClassOf [ GoInformationBiomacromolecule: ];
 }
 <InformationBiomacromolecule> @<ChemicalEntity> AND EXTRA a {
-   a @<InformationBiomacromoleculeClass> +;
-	enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
-	contributes_to: @<MolecularFunction> {0,1};
+  a @<InformationBiomacromoleculeClass> +;
+  enables: ( @<MolecularFunction> OR @<RootMolecularFuntion> ) {0,1};
+  contributes_to: @<MolecularFunction> {0,1};
   located_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> ) {0,1};
   is_active_in: ( @<CellularAnatomicalEntity> OR @<VirionComponent> OR @<RootCellularComponent> ) {0,1};
   part_of: @<ProteinContainingComplex> {0,1};
-	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};	  
+  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};	  
 }// rdfs:comment  "an information biomacromolecule - e.g. a protein or RNA product"
 
 <EvidenceClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {