main-for-release into develop

README.md

@@ -64,6 +64,18 @@ For more background, read our [whitepaper](https://www.semanticarts.com/wp-conte
 Contributing
 ---
 
-As of February 2025, gistBFO is in active development. We hope to refine the mappings over time in accordance with the methodological considerations above. We invite feedback and suggestions in the form of GitHub issues.
+gistBFO is in active development. We hope to refine the mappings over time in accordance with the methodological considerations above. We invite feedback and suggestions in the form of GitHub issues.
 
+<br>
+
+Setting Up the Local Repository
+---
+
+- Clone this repository
+- Run the script `./tools/setup.cmd`. This script will work on Windows, Linux, and Mac. It copies the `./tools/pre-commit` hook into `.git/hooks`, which means it will run before every commit you make to the repository.
+
+The pre-commit hook does several things when you run `git commit`:
 
+- Prevents commits to the branches `develop` and `main`.
+- Runs the serializer. This converts files into a standard Turtle format in order to remove noise in the diffs. As the comments in the file indicate, you should use the pre-approved version of `rdf-toolkit.jar` in this directory, rather than another version that you may have elsewhere on your local drive.
+- Note: Any PR containing unserialized commits will be returned for correction.

gistBFO.ttl

@@ -1,6 +1,7 @@
 # imports: http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl
 # imports: https://w3id.org/semanticarts/ontology/gistCore13.0.0
 
+@prefix : <https://w3id.org/semanticarts/ontology/gistBFO#> .
 @prefix gist: <https://w3id.org/semanticarts/ns/ontology/gist/> .
 @prefix obo: <http://purl.obolibrary.org/obo/> .
 @prefix owl: <http://www.w3.org/2002/07/owl#> .
@@ -55,10 +56,6 @@ obo:BFO_0000194
 	rdfs:subPropertyOf gist:isCategorizedBy ;
 	.
 
-skos:editorialNote
-	a owl:AnnotationProperty ;
-	.
-
 gist:Agreement
 	rdfs:subClassOf obo:BFO_0000145 ;
 	.
@@ -74,7 +71,7 @@ gist:Building
 	.
 
 gist:Category
-	rdfs:subClassOf obo:BFO_0000020 ;
+	rdfs:subClassOf obo:BFO_0000031 ;
 	gist:bfoMappingNote "BFO does not seem to have categories, maybe because everything in BFO is a category."^^xsd:string ;
 	.
 
@@ -96,6 +93,20 @@ gist:Content
 	gist:bfoMappingNote "Content seems to be a proper subset of generically dependent continuant."^^xsd:string ;
 	.
 
+gist:ControlledVocabulary
+	rdfs:subClassOf [
+		a owl:Class ;
+		owl:intersectionOf (
+			obo:BFO_0000031
+			[
+				a owl:Restriction ;
+				owl:onProperty obo:BFO_0000178 ;
+				owl:someValuesFrom obo:BFO_0000031 ;
+			]
+		) ;
+	] ;
+	.
+
 gist:Equipment
 	rdfs:subClassOf obo:BFO_0000030 ;
 	gist:bfoMappingNote "Equipment is clearly a material entity. Initial mapping will map to the object subclass."^^xsd:string ;
@@ -106,49 +117,23 @@ gist:Event
 	.
 
 gist:GeoPoint
-	rdfs:subClassOf [
-		owl:unionOf (
-			obo:BFO_0000018
-			obo:BFO_0000147
-		) ;
-	] ;
-	.
-
-gist:GeoRegion
-	rdfs:subClassOf [
-		owl:unionOf (
-			obo:BFO_0000009
-			obo:BFO_0000146
-		) ;
-	] ;
+	rdfs:subClassOf obo:BFO_0000147 ;
 	.
 
 gist:GeoRoute
-	rdfs:subClassOf [
-		owl:unionOf (
-			obo:BFO_0000009
-			obo:BFO_0000142
-		) ;
-	] ;
+	rdfs:subClassOf obo:BFO_0000142 ;
 	gist:bfoMappingNote "Routes are collections of one dimensional regions, but they may trace out a 2D path."^^xsd:string ;
 	.
 
 gist:GeoSegment
-	rdfs:subClassOf [
-		owl:unionOf (
-			obo:BFO_0000026
-			obo:BFO_0000142
-		) ;
-	] ;
+	rdfs:subClassOf obo:BFO_0000142 ;
 	.
 
 gist:GeoVolume
 	rdfs:subClassOf [
-		owl:unionOf (
-			obo:BFO_0000028
-			obo:BFO_0000029
-			obo:BFO_0000024
-		) ;
+		a owl:Restriction ;
+		owl:onProperty obo:BFO_0000210 ;
+		owl:someValuesFrom obo:BFO_0000028 ;
 	] ;
 	.
 
@@ -158,7 +143,14 @@ gist:IntellectualProperty
 	.
 
 gist:Intention
-	rdfs:subClassOf obo:BFO_0000002 ;
+	rdfs:subClassOf [
+		a owl:Class ;
+		owl:unionOf (
+			obo:BFO_0000020
+			obo:BFO_0000031
+		) ;
+	] ;
+	gist:bfoMappingNote "It is to be determined whether this only holds for mental entities or it can work for, say, BFO:function"^^xsd:string ;
 	.
 
 gist:Language
@@ -194,26 +186,38 @@ gist:OrderedMember
 	.
 
 gist:Organization
-	rdfs:subClassOf obo:BFO_0000141 ;
+	rdfs:subClassOf obo:BFO_0000027 ;
 	gist:bfoMappingNote "Organization is clearly an independent continuant and immaterial. May need to update to be consistent with Common Core Ontology as well."^^xsd:string ;
 	.
 
 gist:PhysicalIdentifiableItem
 	rdfs:subClassOf obo:BFO_0000004 ;
-	skos:bfoMappingNote "A physical identifiable item is a independent continuant that is not a spatial region."^^xsd:string ;
+	gist:bfoMappingNote "A physical identifiable item is a independent continuant that is not a spatial region."^^xsd:string ;
 	.
 
 gist:PhysicalSubstance
 	rdfs:subClassOf obo:BFO_0000040 ;
 	gist:bfoMappingNote "Physical substance is a material entity, but not an object or aggregate as those are physical identifiable items and collections."^^xsd:string ;
 	.
 
+gist:Place
+	rdfs:subClassOf [
+		a owl:Class ;
+		owl:unionOf (
+			obo:BFO_0000029
+			obo:BFO_0000040
+			obo:BFO_0000140
+		) ;
+	] ;
+	.
+
 gist:SchemaMetaData
 	rdfs:subClassOf obo:BFO_0000031 ;
 	.
 
 gist:Specification
 	rdfs:subClassOf obo:BFO_0000031 ;
+	gist:bfoMappingNote "Likely a CCO directive information content entity"^^xsd:string ;
 	.
 
 gist:System
@@ -234,7 +238,8 @@ gist:TimeInterval
 	.
 
 gist:UnitOfMeasure
-	gist:bfoMappingNote "Unclear if unit of measure fits in BFO. To avoid potentially inconsistent ontologies, it is initially not mapped to BFO."^^xsd:string ;
+	rdfs:subClassOf obo:BFO_0000031 ;
+	gist:bfoMappingNote "Mapped under GDC, following CCO"^^xsd:string ;
 	.
 
 gist:bfoMappingNote