From 878330e30d334a09c0ea7243db17120686be4f23 Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Tue, 5 Dec 2023 11:54:37 -0500
Subject: [PATCH 1/3] Replace obsolete native cell with cell

---
 shapes/go-cam-shapes.shex | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex
index 4820566..256b056 100644
--- a/shapes/go-cam-shapes.shex
+++ b/shapes/go-cam-shapes.shex
@@ -62,7 +62,7 @@ PREFIX GoTransporterActivity: <http://purl.obolibrary.org/obo/GO_0005215>
 PREFIX GoChemicalEntity: <http://purl.obolibrary.org/obo/CHEBI_24431>
 PREFIX GoEvidence: <http://purl.obolibrary.org/obo/ECO_0000000>
 PREFIX GoAnatomicalEntity: <http://purl.obolibrary.org/obo/CARO_0000000>
-PREFIX GoNativeCell: <http://purl.obolibrary.org/obo/CL_0000003>
+PREFIX GoCell: <http://purl.obolibrary.org/obo/CL_0000000>
 PREFIX GoOrganism: <http://purl.obolibrary.org/obo/NCBITaxon_1>
 PREFIX GoBiologicalPhase: <http://purl.obolibrary.org/obo/GO_0044848>
 PREFIX GoLifeCycleStage: <http://purl.obolibrary.org/obo/UBERON_0000105>
@@ -489,7 +489,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 } // rdfs:comment  "an anatomical entity"
 
 <NativeCellClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
-  rdfs:subClassOf [ GoNativeCell: ];
+  rdfs:subClassOf [ GoCell: ];
 }
 
 <NativeCell> @<GoCamEntity> AND EXTRA a {

From c3c6a74c206007b9ba334e1dd1bffc0603a1fd5e Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Tue, 5 Dec 2023 12:10:03 -0500
Subject: [PATCH 2/3] Fix additional mentions of native cell

---
 shapes/go-cam-shapes.shex | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/shapes/go-cam-shapes.shex b/shapes/go-cam-shapes.shex
index 256b056..4a49796 100644
--- a/shapes/go-cam-shapes.shex
+++ b/shapes/go-cam-shapes.shex
@@ -241,7 +241,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <CellDifferentiation> @<BiologicalProcess> AND EXTRA a {
   a @<CellDifferentiationClass> {1};
-  results_in_acquisition_of_features_of: @<NativeCell> {0,1};
+  results_in_acquisition_of_features_of: @<Cell> {0,1};
 } // rdfs:comment "a cell differentiation GO biological process or child"
 
 <CellDivisionClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -250,7 +250,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <CellDivision> @<BiologicalProcess> AND EXTRA a {
   a @<CellDivisionClass> {1};
-  has_input: @<NativeCell> {0,1};
+  has_input: @<Cell> {0,1};
 } // rdfs:comment "a cell division GO biological process or child"
 
 <CellFateCommitmentClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -259,7 +259,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <CellFateCommitment> @<BiologicalProcess> AND EXTRA a {
   a @<CellFateCommitmentClass> {1};
-  results_in_commitment_to: @<NativeCell> {0,1};
+  results_in_commitment_to: @<Cell> {0,1};
 } // rdfs:comment "a cell fate commitment GO biological process or child"
 
 <CellFateDeterminationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -268,7 +268,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <CellFateDetermination> @<BiologicalProcess> AND EXTRA a {
   a @<CellFateDeterminationClass> {1};
-  results_in_determination_of: @<NativeCell> {0,1};
+  results_in_determination_of: @<Cell> {0,1};
 } // rdfs:comment "a cell fate determination GO biological process or child"
 
 <CellFateSpecificationClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -277,7 +277,7 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
 
 <CellFateSpecification> @<BiologicalProcess> AND EXTRA a {
   a @<CellFateSpecificationClass> {1};
-  results_in_specification_of: @<NativeCell> {0,1};
+  results_in_specification_of: @<Cell> {0,1};
 } // rdfs:comment "a cell fate specification GO biological process or child"
 
 <CellularComponentAssemblyClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
@@ -488,14 +488,14 @@ PREFIX results_in_remodeling_of: <http://purl.obolibrary.org/obo/RO_0002591>
   location_of: ( @<InformationBiomacromolecule> OR @<ProteinContainingComplex> ) {0,1};
 } // rdfs:comment  "an anatomical entity"
 
-<NativeCellClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
+<CellClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
   rdfs:subClassOf [ GoCell: ];
 }
 
-<NativeCell> @<GoCamEntity> AND EXTRA a {
-  a @<NativeCellClass> {1};
+<Cell> @<GoCamEntity> AND EXTRA a {
+  a @<CellClass> {1};
   part_of: @<AnatomicalEntity> {0,1};
-} // rdfs:comment  "a native cell or child"
+} // rdfs:comment  "a cell or child"
 
 <CellularComponentClass> IRI @<OwlClass> AND EXTRA rdfs:subClassOf {
   rdfs:subClassOf [ GoCellularComponent: ];

From 292b1e003dc0ed2f6eee43441eb80a54d3d77ceb Mon Sep 17 00:00:00 2001
From: Jim Balhoff <jim@balhoff.org>
Date: Thu, 14 Dec 2023 14:08:32 -0500
Subject: [PATCH 3/3] Replace CHEBI term in test.

---
 .../should_pass/Test027-has_input_2_MolecularEntity.ttl     | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl
index 00de798..171fa5e 100644
--- a/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl
+++ b/test_ttl/go_cams/should_pass/Test027-has_input_2_MolecularEntity.ttl
@@ -157,8 +157,8 @@ owl:versionInfo rdf:type owl:AnnotationProperty .
 <http://purl.obolibrary.org/obo/CHEBI_4705> rdf:type owl:Class .
 
 
-###  http://purl.obolibrary.org/obo/CHEBI_60579
-<http://purl.obolibrary.org/obo/CHEBI_60579> rdf:type owl:Class .
+###  http://purl.obolibrary.org/obo/CHEBI_30623
+<http://purl.obolibrary.org/obo/CHEBI_30623> rdf:type owl:Class .
 
 
 ###  http://purl.obolibrary.org/obo/ECO_0000314
@@ -467,7 +467,7 @@ owl:versionInfo rdf:type owl:AnnotationProperty .
 
 ###  http://model.geneontology.org/5d27d1cf00000607/5d27d1cf00000626
 <http://model.geneontology.org/5d27d1cf00000607/5d27d1cf00000626> rdf:type owl:NamedIndividual ,
-                                                                           <http://purl.obolibrary.org/obo/CHEBI_60579> ;
+                                                                           <http://purl.obolibrary.org/obo/CHEBI_30623> ;
                                                                   <http://purl.org/dc/elements/1.1/contributor> "http://orcid.org/0000-0003-1813-6857"^^xsd:string ;
                                                                   <http://purl.org/dc/elements/1.1/date> "2019-07-12"^^xsd:string ;
                                                                   <http://purl.org/pav/providedBy> "http://geneontology.org"^^xsd:string .