From 66cd8fe96afa565b6a576f8665eec43607981d44 Mon Sep 17 00:00:00 2001
From: Krishna Udaiwal <krishna.u@hotmail.com>
Date: Mon, 25 Oct 2021 14:58:18 -0400
Subject: [PATCH 1/2] Removed object_property per issue #117

Updated equivalent classes into subclass relationships
---
 src/ontology/agro-edit.owl   | 12 +++---------
 src/ontology/patterns/eq.owl | 12 +-----------
 2 files changed, 4 insertions(+), 20 deletions(-)

diff --git a/src/ontology/agro-edit.owl b/src/ontology/agro-edit.owl
index e258f70..763d9be 100644
--- a/src/ontology/agro-edit.owl
+++ b/src/ontology/agro-edit.owl
@@ -646,7 +646,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/AGRO_01000019>))
 Declaration(Class(<http://purl.obolibrary.org/obo/AGRO_01000020>))
 Declaration(Class(<http://purl.obolibrary.org/obo/AGRO_01000021>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_00000077>))
-Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AGRO_00000148>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AGRO_00000253>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/uo#is_unit_of>))
 Declaration(DataProperty(<http://purl.obolibrary.org/obo/AGRO_00000417>))
@@ -672,10 +671,6 @@ AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_01000022> "p
 #   Object Properties
 ############################
 
-# Object Property: <http://purl.obolibrary.org/obo/AGRO_00000148> (has method)
-
-AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_00000148> "has method"@en)
-
 # Object Property: <http://purl.obolibrary.org/obo/AGRO_00000253> (measurement method of)
 
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_00000253> "measurement method of"@en)
@@ -1986,7 +1981,6 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_00000192> "mulch thickness"@en)
 EquivalentClasses(<http://purl.obolibrary.org/obo/AGRO_00000192> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/PATO_0000915> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/AGRO_00000092>)))
 SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000192> <http://purl.obolibrary.org/obo/PATO_0000915>)
-SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000192> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/AGRO_00000148> <http://purl.obolibrary.org/obo/AGRO_00000247>))
 
 # Class: <http://purl.obolibrary.org/obo/AGRO_00000194> (mulch color)
 
@@ -2354,8 +2348,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000245> <http://purl.obolibrar
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/AGRO_00000247> "With a ruler measure the distance between the soil surface and the top of the mulch layer."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_00000247> "mulch thickness measurement protocol"@en)
-EquivalentClasses(<http://purl.obolibrary.org/obo/AGRO_00000247> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/AGRO_00000253> <http://purl.obolibrary.org/obo/AGRO_00000192>))
 SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000247> <http://purl.obolibrary.org/obo/OBI_0000272>)
+SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000247> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/AGRO_00000192>))
 
 # Class: <http://purl.obolibrary.org/obo/AGRO_00000248> (interrow width measurement protocol)
 
@@ -2552,8 +2546,8 @@ SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000277> <http://purl.obolibrar
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.obolibrary.org/obo/AGRO_00000278> "Record the color of the mulch applied."@en)
 AnnotationAssertion(rdfs:comment <http://purl.obolibrary.org/obo/AGRO_00000278> "Need to add a standard protocol to measure the color of the mulch, if it exists."@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/AGRO_00000278> "mulch color recording protocol"@en)
-EquivalentClasses(<http://purl.obolibrary.org/obo/AGRO_00000278> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/AGRO_00000253> <http://purl.obolibrary.org/obo/AGRO_00000194>))
 SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000278> <http://purl.obolibrary.org/obo/OBI_0000272>)
+SubClassOf(<http://purl.obolibrary.org/obo/AGRO_00000278> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000052> <http://purl.obolibrary.org/obo/AGRO_00000194>))
 
 # Class: <http://purl.obolibrary.org/obo/AGRO_00000279> (transplant age counting protocol)
 
@@ -5660,4 +5654,4 @@ AnnotationAssertion(owl:deprecated <http://purl.obolibrary.org/obo/AGRO_00010149
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/IAO_0000005> "experiment objective"@en)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000283> "kg/ha"@en)
 AnnotationAssertion(<http://www.geneontology.org/formats/oboInOwl#hasExactSynonym> <http://purl.obolibrary.org/obo/UO_0000323> "t/ha"@en)
-)
+)
\ No newline at end of file
diff --git a/src/ontology/patterns/eq.owl b/src/ontology/patterns/eq.owl
index eee57d6..c865249 100644
--- a/src/ontology/patterns/eq.owl
+++ b/src/ontology/patterns/eq.owl
@@ -46,12 +46,6 @@
     
 
 
-    <!-- http://purl.obolibrary.org/obo/AGRO_00000148 -->
-
-    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/AGRO_00000148"/>
-    
-
-
     <!-- http://purl.obolibrary.org/obo/RO_0000052 -->
 
     <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000052"/>
@@ -328,10 +322,6 @@
             <owl:Class>
                 <owl:intersectionOf rdf:parseType="Collection">
                     <rdf:Description rdf:about="http://purl.obolibrary.org/obo/PATO_0000014"/>
-                    <owl:Restriction>
-                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/AGRO_00000148"/>
-                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/AGRO_00000278"/>
-                    </owl:Restriction>
                     <owl:Restriction>
                         <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000052"/>
                         <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/AGRO_00000092"/>
@@ -669,8 +659,8 @@
                 </owl:intersectionOf>
             </owl:Class>
         </owl:equivalentClass>
-        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">crop residue area density</rdfs:label>
         <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The area density of a crop residue</obo:IAO_0000115>
+        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">crop residue area density</rdfs:label>
     </owl:Class>
     
 

From 8cbcea2760d5b0ca7ae3414d51e656faa5b867a6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Marie-Ang=C3=A9lique=20Laporte?=
 <marieangelique.laporte@gmail.com>
Date: Mon, 4 Apr 2022 10:56:46 +0200
Subject: [PATCH 2/2] removing has method property

as this is not following best practices to create specific properties
---
 src/ontology/agro-edit.owl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/ontology/agro-edit.owl b/src/ontology/agro-edit.owl
index 578bad2..1e7ce8a 100644
--- a/src/ontology/agro-edit.owl
+++ b/src/ontology/agro-edit.owl
@@ -740,8 +740,6 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_91240>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_00000077>))
 Declaration(Class(<http://purl.obolibrary.org/obo/ENVO_00002053>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0001351>))
-Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AGRO_00000148>))
-
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/AGRO_00000253>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/BFO_0000051>))
 Declaration(ObjectProperty(<http://purl.obolibrary.org/obo/RO_0000052>))