backend ObjectProperty refactor part 2

This commit was created by running
`qnamefix {*,{bridge,unused}/*}.ttl` and
`qnamefix -x obo unused/sequence_slim.ttl` at
pyontutils commit 5dccd476e3e7f6817a44494f7f774c45761650bb.

This refactor upgrades all internal NIFSTD modelling to use BFO2.
It also introduces a number of reasoner errors due to incompatibilities
between imported ontologies (e.g. obophenotype/uberon#1370)
Upgrading to newer versions of imports resolves some, but not all of the
issues. These upgrades are on the roadmap.

The AnnotationProperty refactor will come, but it requires significantly
more curation to resolve issues with the multitude of properties used
and it will be more efficient to do so after we deprecate some of the
existing branches of the ontology that now have good community support.

ttl/BIRNLex-OBI-proxy.ttl

@@ -1,6 +1,6 @@
 @prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
+@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
 @prefix BFO1SNAP: <http://www.ifomis.org/bfo/1.1/snap#> .
-@prefix BFO1SPAN: <http://www.ifomis.org/bfo/1.1/span#> .
 @prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
 @prefix dc: <http://purl.org/dc/elements/1.1/> .
 @prefix IAO: <http://purl.obolibrary.org/obo/IAO_> .
@@ -44,7 +44,7 @@ BIRNLEX:6 a owl:Class .
 BIRNLEX:11000 a owl:Class ;
     rdfs:label "Non-realizable information entity"^^xsd:string ;
     skos:prefLabel "Non-realizable information entity"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000031> ;
+    rdfs:subClassOf BFO:0000031 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -122,7 +122,7 @@ BIRNLEX:11006 a owl:Class ;
 BIRNLEX:11007 a owl:Class ;
     rdfs:label "Information entity"^^xsd:string ;
     skos:prefLabel "Information entity"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000031> ;
+    rdfs:subClassOf BFO:0000031 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -171,7 +171,7 @@ BIRNLEX:11011 a owl:Class ;
     rdfs:label "Digital entity"^^xsd:string ;
     skos:prefLabel "Digital entity"^^xsd:string ;
     skos:definition "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical. (OBI)"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000031> ;
+    rdfs:subClassOf BFO:0000031 ;
     rdfs:comment "OBI has this as a child of \"non realizable information entity\"; we may need to update the entire hierarchy (Maryann Martone)."^^xsd:string ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
@@ -204,7 +204,7 @@ BIRNLEX:11012 a owl:Class ;
 BIRNLEX:11013 a owl:Class ;
     rdfs:label "Disease"^^xsd:string ;
     skos:prefLabel "Disease"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000016> ;
+    rdfs:subClassOf BFO:0000016 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -216,7 +216,7 @@ BIRNLEX:11013 a owl:Class ;
 BIRNLEX:11014 a owl:Class ;
     rdfs:label "Investigation administration role"^^xsd:string ;
     skos:prefLabel "Investigation administration role"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000023> ;
+    rdfs:subClassOf BFO:0000023 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -238,7 +238,7 @@ BIRNLEX:11015 a owl:Class ;
 BIRNLEX:11016 a owl:Class ;
     rdfs:label "Role in protocol application"^^xsd:string ;
     skos:prefLabel "Role in protocol application"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000023> ;
+    rdfs:subClassOf BFO:0000023 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2008-02-21"^^xsd:string ;
@@ -275,7 +275,7 @@ BIRNLEX:11018 a owl:Class ;
 BIRNLEX:11019 a owl:Class ;
     rdfs:label "Reagent role"^^xsd:string ;
     skos:prefLabel "Reagent role"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000023> ;
+    rdfs:subClassOf BFO:0000023 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -298,7 +298,7 @@ BIRNLEX:11020 a owl:Class ;
 BIRNLEX:11021 a owl:Class ;
     rdfs:label "Planned process"^^xsd:string ;
     skos:prefLabel "Planned process"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000015> ;
+    rdfs:subClassOf BFO:0000015 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -380,7 +380,7 @@ BIRNLEX:11028 a owl:Class ;
     rdfs:label "Artefact entity"^^xsd:string ;
     skos:prefLabel "Artefact object"^^xsd:string ;
     NIFRID:synonym "artefact object"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000040> ;
+    rdfs:subClassOf BFO:0000040 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2007-10-05"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-05"^^xsd:string ;
@@ -558,7 +558,7 @@ BIRNLEX:11042 a owl:Class ;
 BIRNLEX:11043 a owl:Class ;
     rdfs:label "Reference"^^xsd:string ;
     skos:prefLabel "Reference"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000023> ;
+    rdfs:subClassOf BFO:0000023 ;
     skos:editorialNote "This is a proxy class to be replaced by its OBI equivalent, once there is an official release built off BFO v1.1 that can be successfully classified using Pellet v1.5.0 in Protege."^^xsd:string ;
     NIFRID:createdDate "2008-02-21"^^xsd:string ;
     NIFRID:modifiedDate "2008-02-21"^^xsd:string ;

ttl/BIRNLex-OBO-UBO.ttl

@@ -1,6 +1,8 @@
 @prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
+@prefix bearerOf: <http://purl.obolibrary.org/obo/RO_0000053> .
 @prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
 @prefix dc: <http://purl.org/dc/elements/1.1/> .
+@prefix inheresIn: <http://purl.obolibrary.org/obo/RO_0000052> .
 @prefix NIFEXT: <http://uri.neuinfo.org/nif/nifstd/nifext_> .
 @prefix NIFRID: <http://uri.neuinfo.org/nif/nifstd/readable/> .
 @prefix NLXANAT: <http://uri.neuinfo.org/nif/nifstd/nlx_anat_> .
@@ -46,20 +48,20 @@
 
 ### Object Properties
 
-<http://purl.obolibrary.org/obo/RO_0000052> a owl:FunctionalProperty,
-        owl:ObjectProperty ;
-    rdfs:label "inheres_in"@en ;
-    rdfs:comment "Examples: the redness inhering in an eye of a wild-type fruitfly"^^xsd:string .
-
-<http://purl.obolibrary.org/obo/RO_0000053> a owl:ObjectProperty ;
+bearerOf: a owl:ObjectProperty ;
     rdfs:label "is_bearer_of"^^xsd:string ;
     skos:prefLabel "is_bearer_of"^^xsd:string ;
-    owl:inverseOf <http://purl.obolibrary.org/obo/RO_0000052> ;
+    owl:inverseOf inheresIn: ;
     NIFRID:createdDate "2007-10-02"^^xsd:string ;
     NIFRID:modifiedDate "2007-10-02"^^xsd:string ;
     NIFRID:hasBirnlexCurator NIFRID:Bill_Bug ;
     NIFRID:tempDefinition "Makes it possible for an independent_continuant to represent its relation to a dependent_continuant, such as a PATO quality, a bfo:disposition, or a bfo:function."^^xsd:string .
 
+inheresIn: a owl:FunctionalProperty,
+        owl:ObjectProperty ;
+    rdfs:label "inheres_in"@en ;
+    rdfs:comment "Examples: the redness inhering in an eye of a wild-type fruitfly"^^xsd:string .
+
 ### Classes
 
 BIRNLEX:5 a owl:Class ;

ttl/NIF-Cell.ttl

@@ -1,5 +1,5 @@
 @prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
-@prefix BFO1SNAP: <http://www.ifomis.org/bfo/1.1/snap#> .
+@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
 @prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
 @prefix dc: <http://purl.org/dc/elements/1.1/> .
 @prefix NIFEXT: <http://uri.neuinfo.org/nif/nifstd/nifext_> .
@@ -3751,7 +3751,7 @@ SAO:1813327414 a owl:Class ;
     rdfs:label "Cell"^^xsd:string ;
     skos:prefLabel "Cell"^^xsd:string ;
     skos:definition "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope (Gene Ontology)."^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000040> ;
+    rdfs:subClassOf BFO:0000040 ;
     rdfs:comment "We are restricting ourselves to cells that are in the nervous system or closely associated with nervous system cells, e.g., muscle cells. A more complete ontology of Cell Types is available through OBO. Eventually, we hope to provide our contents to OBO Cell Type."^^xsd:string ;
     NIFRID:modifiedDate "December 5, 2008"^^xsd:string ;
     NIFRID:cell_ontology_ID "CL:0000000"^^xsd:string ;

ttl/NIF-DOID-Bridge.ttl

@@ -1,5 +1,5 @@
 @prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
-@prefix BFO1SNAP: <http://www.ifomis.org/bfo/1.1/snap#> .
+@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
 @prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
 @prefix DOID: <http://purl.obolibrary.org/obo/DOID_> .
 @prefix NLXDYS: <http://uri.neuinfo.org/nif/nifstd/nlx_dys_> .
@@ -16,6 +16,8 @@
 
 ### Classes
 
+BFO:0000016 a owl:Class .
+
 BIRNLEX:2086 a owl:Class ;
     owl:equivalentClass DOID:1289 .
 
@@ -563,7 +565,7 @@ BIRNLEX:12831 a owl:Class ;
     owl:equivalentClass DOID:14503 .
 
 DOID:4 a owl:Class ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000016> .
+    rdfs:subClassOf BFO:0000016 .
 
 DOID:168 a owl:Class .
 
@@ -932,8 +934,6 @@ DOID:14777 a owl:Class .
 
 DOID:0050742 a owl:Class .
 
-<http://purl.obolibrary.org/obo/BFO_0000016> a owl:Class .
-
 NLXDYS:090801 a owl:Class ;
     owl:equivalentClass DOID:11870 .
 

ttl/NIF-Dysfunction.ttl

@@ -1,5 +1,5 @@
 @prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
-@prefix BFO1SNAP: <http://www.ifomis.org/bfo/1.1/snap#> .
+@prefix BFO: <http://purl.obolibrary.org/obo/BFO_> .
 @prefix BIRNLEX: <http://uri.neuinfo.org/nif/nifstd/birnlex_> .
 @prefix dc: <http://purl.org/dc/elements/1.1/> .
 @prefix NIFRID: <http://uri.neuinfo.org/nif/nifstd/readable/> .
@@ -142,7 +142,7 @@ BIRNLEX:2104 a owl:Class ;
 
 BIRNLEX:11013 a owl:Class ;
     rdfs:label "Disease"^^xsd:string ;
-    rdfs:subClassOf <http://purl.obolibrary.org/obo/BFO_0000016> .
+    rdfs:subClassOf BFO:0000016 .
 
 BIRNLEX:12500 a owl:Class ;
     rdfs:label "Huntingtons disease"^^xsd:string ;