Merge pull request #108 from mcwdsi/issue-83

fixing obsolete classes from OBI that were moved to COB. Fixes #83

Author: hoganwr

src/ontology/dron-edit.owl

@@ -293,10 +293,10 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0032501>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0050886>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000009>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000011>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000047>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000035>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000026>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000576>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100026>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000022>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000090>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000125>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000000001>))
@@ -937,7 +937,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/DRON_00000028> "William R. Hogan"@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/DRON_00000028> "active ingredient"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000028> <http://purl.obolibrary.org/obo/DRON_00000030>)
-SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000028> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000054> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/DRON_00000031>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/OBI_0000576>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/OBI_0100026>))))))
+SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000028> ObjectAllValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000054> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> <http://purl.obolibrary.org/obo/DRON_00000031>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/BFO_0000051> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/BFO_0000015> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/OBI_0000576>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/COB_0000022>))))))
 
 # Class: <http://purl.obolibrary.org/obo/DRON_00000029> (excipient)
 
@@ -967,7 +967,7 @@ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000115> <http://purl.ob
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/DRON_00000031> "William R. Hogan"@en)
 AnnotationAssertion(rdfs:label <http://purl.obolibrary.org/obo/DRON_00000031> "drug administration"@en)
 SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000031> <http://purl.obolibrary.org/obo/OGMS_0000090>)
-SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000031> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OGMS_0000090> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/DRON_00000005>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/OBI_0100026>)))
+SubClassOf(<http://purl.obolibrary.org/obo/DRON_00000031> ObjectIntersectionOf(<http://purl.obolibrary.org/obo/OGMS_0000090> ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/DRON_00000005>) ObjectSomeValuesFrom(<http://purl.obolibrary.org/obo/RO_0000057> <http://purl.obolibrary.org/obo/COB_0000022>)))
 
 # Class: <http://purl.obolibrary.org/obo/DRON_00000032> (drug product therapeutic function)
 
@@ -2130,25 +2130,25 @@ SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000009> <http://purl.obolibrary.
 
 SubClassOf(<http://purl.obolibrary.org/obo/IAO_0000030> <http://purl.obolibrary.org/obo/BFO_0000031>)
 
-# Class: <http://purl.obolibrary.org/obo/OBI_0000011> (obsolete planned process)
+# Class: <http://purl.obolibrary.org/obo/COB_0000035> (obsolete planned process)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000011> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/COB_0000035> <http://purl.obolibrary.org/obo/IAO_0000122>)
 
-# Class: <http://purl.obolibrary.org/obo/OBI_0000047> (obsolete processed material)
+# Class: <http://purl.obolibrary.org/obo/COB_0000026> (obsolete processed material)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000047> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/COB_0000026> <http://purl.obolibrary.org/obo/IAO_0000122>)
 
 # Class: <http://purl.obolibrary.org/obo/OBI_0000576> (scattered molecular aggregate)
 
 AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0000576> <http://purl.obolibrary.org/obo/IAO_0000123>)
 
-# Class: <http://purl.obolibrary.org/obo/OBI_0100026> (obsolete organism)
+# Class: <http://purl.obolibrary.org/obo/COB_0000022> (obsolete organism)
 
-AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/OBI_0100026> <http://purl.obolibrary.org/obo/IAO_0000122>)
+AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000114> <http://purl.obolibrary.org/obo/COB_0000022> <http://purl.obolibrary.org/obo/IAO_0000122>)
 
 # Class: <http://purl.obolibrary.org/obo/OGMS_0000090> (treatment)
 
-SubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000090> <http://purl.obolibrary.org/obo/OBI_0000011>)
+SubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000090> <http://purl.obolibrary.org/obo/COB_0000035>)
 
 # Class: <http://purl.obolibrary.org/obo/PATO_0000125> (mass)
 

src/ontology/imports/external_import.owl

@@ -54,6 +54,9 @@ Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_7660>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_7872>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_8378>))
 Declaration(Class(<http://purl.obolibrary.org/obo/CHEBI_8461>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000022>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000026>))
+Declaration(Class(<http://purl.obolibrary.org/obo/COB_0000035>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0003008>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005488>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0005515>))
@@ -63,10 +66,7 @@ Declaration(Class(<http://purl.obolibrary.org/obo/GO_0032501>))
 Declaration(Class(<http://purl.obolibrary.org/obo/GO_0050886>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000003>))
 Declaration(Class(<http://purl.obolibrary.org/obo/IAO_0000009>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000011>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000047>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0000576>))
-Declaration(Class(<http://purl.obolibrary.org/obo/OBI_0100026>))
 Declaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000090>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PATO_0000125>))
 Declaration(Class(<http://purl.obolibrary.org/obo/PR_000000001>))

src/ontology/imports/obi_import.owl

@@ -19,10 +19,7 @@ Annotation(owl:versionInfo "2026-01-31")
 
 Declaration(Class(obo:BFO_0000040))
 Declaration(Class(obo:IAO_0000030))
-Declaration(Class(obo:OBI_0000011))
-Declaration(Class(obo:OBI_0000047))
 Declaration(Class(obo:OBI_0000576))
-Declaration(Class(obo:OBI_0100026))
 Declaration(ObjectProperty(obo:BFO_0000051))
 Declaration(ObjectProperty(obo:OBI_0000643))
 Declaration(ObjectProperty(obo:OBI_0001938))
@@ -35,7 +32,6 @@ Declaration(AnnotationProperty(obo:IAO_0000116))
 Declaration(AnnotationProperty(obo:IAO_0000117))
 Declaration(AnnotationProperty(obo:IAO_0000118))
 Declaration(AnnotationProperty(obo:IAO_0000119))
-Declaration(AnnotationProperty(obo:IAO_0000232))
 Declaration(AnnotationProperty(dc:source))
 
 ############################
@@ -85,29 +81,6 @@ AnnotationAssertion(rdfs:label obo:OBI_0001937 "has specified numeric value")
 #   Classes
 ############################
 
-# Class: obo:OBI_0000011 (obsolete planned process)
-
-AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000011 "obsolete planned process")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000011 "Injecting mice with a vaccine in order to test its efficacy")
-AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000011 obo:IAO_0000122)
-AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000011 "A process that realizes a plan which is the concretization of a plan specification."@en)
-AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000011 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)")
-AnnotationAssertion(obo:IAO_0000116 obo:OBI_0000011 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process.")
-AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000011 "Bjoern Peters")
-AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000011 "branch derived")
-AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000011 "6/11/9: Edited at workshop. Used to include: is initiated by an agent")
-AnnotationAssertion(obo:IAO_0000232 obo:OBI_0000011 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)")
-AnnotationAssertion(rdfs:label obo:OBI_0000011 "obsolete planned process")
-
-# Class: obo:OBI_0000047 (obsolete processed material)
-
-AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000047 "obsolete processed material")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0000047 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples")
-AnnotationAssertion(obo:IAO_0000114 obo:OBI_0000047 obo:IAO_0000122)
-AnnotationAssertion(obo:IAO_0000115 obo:OBI_0000047 "Is a material entity that is created or changed during material processing."@en)
-AnnotationAssertion(obo:IAO_0000117 obo:OBI_0000047 "PERSON: Alan Ruttenberg")
-AnnotationAssertion(rdfs:label obo:OBI_0000047 "obsolete processed material")
-
 # Class: obo:OBI_0000576 (scattered molecular aggregate)
 
 AnnotationAssertion(obo:IAO_0000111 obo:OBI_0000576 "scattered molecular aggregate")
@@ -120,20 +93,5 @@ AnnotationAssertion(obo:IAO_0000119 obo:OBI_0000576 "Discussion in Karslruhe wit
 AnnotationAssertion(rdfs:label obo:OBI_0000576 "scattered molecular aggregate"@en)
 SubClassOf(obo:OBI_0000576 obo:BFO_0000040)
 
-# Class: obo:OBI_0100026 (obsolete organism)
-
-AnnotationAssertion(obo:IAO_0000111 obo:OBI_0100026 "obsolete organism")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0100026 "animal")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0100026 "fungus")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0100026 "plant")
-AnnotationAssertion(obo:IAO_0000112 obo:OBI_0100026 "virus")
-AnnotationAssertion(obo:IAO_0000114 obo:OBI_0100026 obo:IAO_0000122)
-AnnotationAssertion(obo:IAO_0000115 obo:OBI_0100026 "A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs."@en)
-AnnotationAssertion(obo:IAO_0000116 obo:OBI_0100026 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')")
-AnnotationAssertion(obo:IAO_0000116 obo:OBI_0100026 "13-02-2009: OBI doesn't take position as to  when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI.")
-AnnotationAssertion(obo:IAO_0000117 obo:OBI_0100026 "GROUP: OBI Biomaterial Branch")
-AnnotationAssertion(obo:IAO_0000119 obo:OBI_0100026 "WEB: http://en.wikipedia.org/wiki/Organism")
-AnnotationAssertion(rdfs:label obo:OBI_0100026 "obsolete organism")
-
 
 )