Merge pull request #39 from BFO-Mappings/release/v2025-01-19

Release v2025-01-19
BFO-Mappings · Jan 19, 2025 · 067e886 · 067e886
2 parents a7b7bbd + 413a17a
commit 067e886
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diff --git a/catalog-v001.xml b/catalog-v001.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+    <uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-bfo-directmappings.ttl" uri="prov-bfo-directmappings.ttl"/>
+    <group id="Folder Repository, directory=, recursive=true, Auto-Update=false, version=2" prefer="public" xml:base=""/>
+</catalog>
diff --git a/prov-bfo-directmappings.ttl b/prov-bfo-directmappings.ttl
@@ -11,12 +11,13 @@
 <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl>
   a                     owl:Ontology;
   rdfs:label            "Basic Formal Ontology (BFO) ISO 21838-2:2020 mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
+  owl:versionIRI        <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-bfo-directmappings.ttl> ;
   dc:contributor        "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;
   dc:license            <https://creativecommons.org/publicdomain/zero/1.0/> ;
-  prov:wasDerivedFrom   <http://www.w3.org/ns/prov> ,
-                        <https://github.com/bfo-ontology/bfo-2020> ;
-  rdfs:seeAlso          <https://basic-formal-ontology.org/> ,
+  prov:wasDerivedFrom   <https://www.w3.org/ns/prov-o-20130430> ,
+                        <https://raw.githubusercontent.com/BFO-ontology/BFO-2020/release-2024-01-29/src/owl/bfo-core.ttl> ;
+  rdfs:seeAlso          <https://www.w3.org/TR/prov-o/>,
+                        <https://basic-formal-ontology.org/> ,
                         <https://github.com/BFO-Mappings/PROV-to-BFO> ;
 .
 
@@ -104,6 +105,15 @@ prov:InstantaneousEvent rdf:type owl:Class .
     rdfs:comment "A prov:InstantaneousEvent is equivalent to a process boundary because it is referred to as the boundary (start or end) of a prov:Activity as an occurrent."@en .
 
 
+prov:Bundle rdf:type owl:Class .
+[]  rdf:type owl:Axiom ;
+    owl:annotatedSource   prov:Bundle ;
+    owl:annotatedProperty rdfs:subClassOf ; 
+    owl:annotatedTarget   obo:BFO_0000031 ;
+    sssom:object_label    "generically dependent continuant" ;
+    rdfs:comment "A prov:Bundle exists in virtue of the fact that there is at least one of what may be multiple copies; it is the content or the pattern that the multiple copies share."@en .
+
+
 prov:Plan rdf:type owl:Class .
 []  rdf:type owl:Axiom ;
     owl:annotatedSource   prov:Plan ;
@@ -167,11 +177,11 @@ prov:DictionaryInvolvement rdf:type owl:Class .
 
 
 # PROV object property mappings
-prov:hadMember rdf:type owl:ObjectProperty . obo:BFO_00000178 rdf:type owl:ObjectProperty .
+prov:hadMember rdf:type owl:ObjectProperty . obo:BFO_0000178 rdf:type owl:ObjectProperty .
 []  rdf:type owl:Axiom ;
     owl:annotatedSource   prov:hadMember ;
     owl:annotatedProperty rdfs:subPropertyOf ;
-    owl:annotatedTarget   obo:BFO_00000178 ;
+    owl:annotatedTarget   obo:BFO_0000178 ;
     sssom:object_label    "has continuant part" ;
     rdfs:comment "A prov:Collection that has member some prov:Entity also has it as a continuant part."@en .
 
@@ -294,11 +304,11 @@ prov:hadUsage rdf:type owl:ObjectProperty . obo:BFO_0000121 rdf:type owl:ObjectP
 
 
 # PROV-Dictionary object property mappings
-prov:hadDictionaryMember rdf:type owl:ObjectProperty . obo:BFO_00000178 rdf:type owl:ObjectProperty .
+prov:hadDictionaryMember rdf:type owl:ObjectProperty . obo:BFO_0000178 rdf:type owl:ObjectProperty .
 []  rdf:type owl:Axiom ;
     owl:annotatedSource   prov:hadDictionaryMember ;
     owl:annotatedProperty rdfs:subPropertyOf ;
-    owl:annotatedTarget   obo:BFO_00000178 ;
+    owl:annotatedTarget   obo:BFO_0000178 ;
     sssom:object_label    "has continuant part (at some time)" ;
     rdfs:comment "A prov:Dictionary has a prov:Key-Entity Pair as a member, then it has it as a continuant part."@en .
 

diff --git a/prov-cco-directmappings.ttl b/prov-cco-directmappings.ttl
@@ -13,14 +13,17 @@
 <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl>
   a                     owl:Ontology;
   rdfs:label            "Common Core Ontologies (CCO) mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
-  owl:imports           <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> ;
-  rdfs:comment          "This mapping depends on the imported PROV-O to BFO mapping" ;
+  owl:versionIRI        <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-cco-directmappings.ttl> ;
   dc:contributor        "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;
   dc:license            <https://creativecommons.org/publicdomain/zero/1.0/> ;
-  prov:wasDerivedFrom   <http://www.w3.org/ns/prov> ,
-                        <https://github.com/CommonCoreOntology/CommonCoreOntologies> ;
-  rdfs:seeAlso          <https://basic-formal-ontology.org/> ,
+  prov:wasDerivedFrom   <https://www.w3.org/ns/prov-o-20130430> ,
+                        <https://raw.githubusercontent.com/BFO-ontology/BFO-2020/release-2024-01-29/src/owl/bfo-core.ttl> ,
+                        <https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/refs/tags/v2.0-2024-11-06/src/cco-merged/CommonCoreOntologiesMerged.ttl> ;
+  rdfs:comment          "This mapping depends on the imported PROV-O to BFO mapping" ;
+  owl:imports           <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-bfo-directmappings.ttl> ;
+  rdfs:seeAlso          <https://www.w3.org/TR/prov-o/>,
+                        <https://basic-formal-ontology.org/> ,
+                        <https://github.com/CommonCoreOntology/CommonCoreOntologies> ,
                         <https://github.com/BFO-Mappings/PROV-to-BFO> ;
 .
 
@@ -48,7 +51,7 @@ prov:Person rdf:type owl:Class .
     owl:annotatedTarget   [ owl:intersectionOf ( cco:ont00001262
                                                  prov:Agent)] ;
     sssom:object_label    "Person" ;
-    rdfs:comment "Every prov:Person is both a prov:Agent and a cco:ont00001262. However, not every cco:ont00001262 is a prov:Agent or cco:ont00001017. So, prov:Person and cco:ont00001262 are not coextensive."@en .
+    rdfs:comment "Every prov:Person is both a prov:Agent and a CCO Person. However, not every CCO Person is a prov:Agent or CCO Agent. So, prov:Person and CCO Person are not coextensive."@en .
 
 
 prov:Organization rdf:type owl:Class .
@@ -58,16 +61,25 @@ prov:Organization rdf:type owl:Class .
     owl:annotatedTarget   [ owl:intersectionOf ( cco:ont00001180
                                                  prov:Agent)] ;
     sssom:object_label    "Organization" ;
-    rdfs:comment "Every prov:Organization is both a prov:Agent and a cco:ont00001180. However, not every cco:ont00001180 is a prov:Agent or cco:ont00001017. So, prov:Organization and cco:ont00001180 are not coextensive."@en .
+    rdfs:comment "Every prov:Organization is both a prov:Agent and a CCO Organization. However, not every CCO Organization is a prov:Agent or CCO Agent. So, prov:Organization and CCO Organization are not coextensive."@en .
 
 
+prov:Bundle rdf:type owl:Class .
+[]  rdf:type owl:Axiom ;
+    owl:annotatedSource   prov:Bundle ;
+    owl:annotatedProperty rdfs:subClassOf ; 
+    owl:annotatedTarget   cco:ont00000958 ;
+    sssom:object_label    "Information Content Entity" ;
+    rdfs:comment "A prov:Bundle is information content which is about entities."@en .
+
+
 prov:Plan rdf:type owl:Class .
 []  rdf:type owl:Axiom ;
     owl:annotatedSource   prov:Plan ;
     owl:annotatedProperty rdfs:subClassOf ; 
     owl:annotatedTarget   cco:ont00000958 ;
     sssom:object_label    "Information Content Entity" ;
-    rdfs:comment "Plans are information content which are about entities. prov:Plan is similar to cco:ont00000974, except that PROV explicitly does not constrain the type of information content that prov:Plans consist of."@en .
+    rdfs:comment "A prov:Plan is information content which is about entities. prov:Plan is similar to CCO Plan, except that PROV explicitly does not constrain the type of information content that PROV plans consist of."@en .
 
 
 prov:Start rdf:type owl:Class .
@@ -76,7 +88,7 @@ prov:Start rdf:type owl:Class .
     owl:annotatedProperty owl:equivalentClass ; 
     owl:annotatedTarget   cco:ont00000197 ;
     sssom:object_label    "Process Beginning" ;
-    rdfs:comment "TODO add justification"@en .
+    rdfs:comment "PROV-O treats a PROV Start as an instantaneous event connected to a particular activity via the Qualification Property PROV qualifiedStart, subject to further restrictions by particular triggering entities, locations, time data, and so on. So, PROV Start can be matched to CCO process beginning. A process beginning is a process boundary occurring on the starting instant of the temporal period occupied by a process that is equivalent to PROV Activity"@en .
 
 
 prov:End rdf:type owl:Class .
@@ -85,7 +97,7 @@ prov:End rdf:type owl:Class .
     owl:annotatedProperty owl:equivalentClass ; 
     owl:annotatedTarget   cco:ont00000083 ;
     sssom:object_label    "Process Ending" ;
-    rdfs:comment "TODO add justification"@en .
+    rdfs:comment "PROV-O treats a PROV End as an instantaneous event connected to a particular activity via the Qualification Property PROV qualifiedEnd, subject to further restrictions by particular triggering entities, locations, time data, and so on. So, PROV End can be matched to CCO process ending. A process ending is a process boundary occurring on the ending instant of the temporal period occupied by a process that is equivalent to PROV Activity"@en .
 
 
 # PROV-Dictionary class mappings

diff --git a/prov-ro-directmappings.ttl b/prov-ro-directmappings.ttl
@@ -11,14 +11,17 @@
 <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl>
   a                     owl:Ontology;
   rdfs:label            "Relation Ontology (RO) mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
-  owl:imports           <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> ;
-  rdfs:comment          "This mapping depends on the imported PROV-O to BFO mapping." ;
+  owl:versionIRI        <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-ro-directmappings.ttl> ;
   dc:contributor        "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;
   dc:license            <https://creativecommons.org/publicdomain/zero/1.0/> ;
-  prov:wasDerivedFrom   <http://www.w3.org/ns/prov> ,
-                        <https://obofoundry.org/ontology/ro.html> ;
-  rdfs:seeAlso          <https://basic-formal-ontology.org/> ,
+  prov:wasDerivedFrom   <https://www.w3.org/ns/prov-o-20130430> ,
+                        <https://raw.githubusercontent.com/BFO-ontology/BFO-2020/release-2024-01-29/src/owl/bfo-core.ttl> ,
+                        <https://raw.githubusercontent.com/oborel/obo-relations/refs/tags/v2024-04-24/ro.owl> ;
+  rdfs:comment          "This mapping depends on the imported PROV-O to BFO mapping." ;
+  owl:imports           <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/refs/tags/v2025-01-19/prov-bfo-directmappings.ttl> ;
+  rdfs:seeAlso          <https://www.w3.org/TR/prov-o/>,
+                        <https://basic-formal-ontology.org/> ,
+                        <https://obofoundry.org/ontology/ro.html> ,
                         <https://github.com/BFO-Mappings/PROV-to-BFO> ;
 .
 

diff --git a/src/Makefile b/src/Makefile
@@ -9,12 +9,13 @@
 # --------------------------------------------------------------------------------
 #### Configuration / details about our project
 # Project essentials
-config.ONTOLOGY_FILE	:= prov-mappings-edit.ttl
-config.ONTOLOGY_PREFIX	:= prov-bfo-directmappings
-config.ONTOLOGY-IRI		:= https://github.com/BFO-Mappings/PROV-to-BFO
-config.BASE_IRI			:= $(config.ONTOLOGY-IRI)_
-config.DEV_IRI			:= $(config.ONTOLOGY-IRI)/dev
-config.MODULES_IRI		:= $(config.DEV_IRI)/modules
+config.ONTOLOGY_FILE		:= prov-mappings-edit.ttl
+config.ONTOLOGY_PREFIX		:= prov-bfo-directmappings
+config.ONTOLOGY_IRI			:= https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main
+config.BASE_IRI				:= $(config.ONTOLOGY_IRI)_
+config.DEV_IRI				:= $(config.ONTOLOGY_IRI)/dev
+config.MODULES_IRI			:= $(config.DEV_IRI)/modules
+config.ALIGNMENT_FILES		:= prov-bfo-directmappings.ttl prov-ro-directmappings.ttl prov-cco-directmappings.ttl
 
 # Local project directories
 config.SOURCE_DIR				:= /
@@ -51,9 +52,10 @@ REQUIRED_DIRS = $(config.TEMP_DIR) $(config.LIBRARY_DIR) $(config.SOURCE_DIR) $(
 
 # --------------------------------------------------------------------------------
 #### Custom targets
-MAPPINGS_FILE			:= prov-bfo-mappings.sssom.csv # csv for importing into google sheets
-mappings: 
-	$(ROBOT) query --input $(EDITOR_BUILD_FILE) -q $(config.QUERIES_DIR)/get-mappings.rq $(MAPPINGS_FILE) --use-graphs true
+SSSOM_FILE			:= $(config.TEMP_DIR)/prov-bfo-mappings.sssom.csv # csv for importing into google sheets
+SSSOM: 
+	$(ROBOT) relax --input $(EDITOR_BUILD_FILE) --include-subclass-of true \
+	query -q $(config.QUERIES_DIR)/SSSOM-mappings.rq $(SSSOM_FILE) --use-graphs true
 
 candidates:
 	$(ROBOT) query --input $(EDITOR_BUILD_FILE) -q $(config.QUERIES_DIR)/candidate-superproperties.rq $(config.TEMP_DIR)/candidate-superproperties.tsv --use-graphs true ;
@@ -65,25 +67,33 @@ candidates-complex:
 # Axioms to materialize in reasoning
 AXIOM_GENERATORS = "SubClass EquivalentClass SubObjectProperty EquivalentObjectProperty InverseObjectProperties"
 
-# Check for unmapped terms after materializing inferred mappings (after removing individuals)
+# Check for unmapped terms after materializing entailed mappings (after removing individuals)
 unmapped:
 	$(ROBOT) remove --input $(EDITOR_BUILD_FILE) --select individuals \
 	reason --reasoner HermiT --axiom-generators "SubClass SubObjectProperty InverseObjectProperties" --include-indirect true \
 	query --output-dir $(config.TEMP_DIR) --queries $(config.QUERIES_DIR)/unmapped-terms.rq --use-graph true
 
-# Materialize all mappings as a list
-inferred-mappings:
+# Materialize all entailed mappings
+# TODO: Make ROBOT filter SWRL rules
+ENTAILED_MAPPINGS_FILENAME = $(config.ONTOLOGY_IRI)/$(config.TEMP_DIR)/all-entailed-mappings
+entailed-mappings:
 	$(ROBOT) remove --input $(EDITOR_BUILD_FILE) --select individuals \
-	reason --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true \
-	query --output-dir $(config.TEMP_DIR) --queries $(config.QUERIES_DIR)/inferred-mappings.rq --use-graph true
+	reason --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true --remove-redundant-subclass-axioms false --exclude-duplicate-axioms true \
+	merge --catalog catalog-v001.xml --collapse-import-closure false --input "../prov-bfo-directmappings.ttl" --input "../prov-cco-directmappings.ttl" --input "../prov-ro-directmappings.ttl" \
+	remove --axioms external --base-iri http://www.w3.org/ns/prov# --base-iri http://www.w3.org/2003/11/swrl# --base-iri http://swrl.stanford.edu/ontologies/3.3/swrla.owl# --select "imports ontology" --trim false \
+	annotate --ontology-iri $(ENTAILED_MAPPINGS_FILENAME).ttl --version-iri $(ENTAILED_MAPPINGS_FILENAME).ttl --annotation owl:versionInfo $(TODAY) \
+	--annotation rdfs:comment "This file was generated using ROBOT and the HermiT reasoner from the PROV-BFO alignments" \
+	--annotation rdfs:comment "Note that this does not include SWRL rules but may in future versions." \
+	--annotation prov:wasDerivedFrom $(config.ONTOLOGY_IRI)/src/prov-mappings-edit.ttl \
+	--output $(config.TEMP_DIR)/all-entailed-mappings.ttl 
 
 # Materialize old and new entailments, then compare the differences. This doesn't include disjoint axioms.
 deductive-diff:
 	$(ROBOT) remove --input $(EDITOR_BUILD_FILE) --select individuals \
-	reason --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true \
+	reason --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true --equivalent-classes-allowed all \
 	query --query $(config.CONSTRUCT_QUERIES_DIR)/prov-triples.rq $(config.TEMP_DIR)/new-prov-triples.ttl --use-graph true 
 
-	$(ROBOT) reason --input $(config.IMPORTS_DIR)/PROV/prov-ontologies.ttl --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true \
+	$(ROBOT) reason --input $(config.IMPORTS_DIR)/PROV/prov-ontologies.ttl --reasoner HermiT --axiom-generators $(AXIOM_GENERATORS) --include-indirect true --equivalent-classes-allowed all \
 	query --query $(config.CONSTRUCT_QUERIES_DIR)/prov-triples.rq $(config.TEMP_DIR)/old-prov-triples.ttl --use-graph true 
 	$(ROBOT) diff --left $(config.TEMP_DIR)/old-prov-triples.ttl --right $(config.TEMP_DIR)/new-prov-triples.ttl --output $(config.TEMP_DIR)/deductive-diff.txt
 
@@ -180,8 +190,8 @@ $(RELEASE_BUILD_FILE): $(EDITOR_BUILD_FILE)
 
 # Function (aka "canned recipe") using parameters to build arguments for `annnotate`
 define annotation-inputs
-	--ontology-iri "$(config.ONTOLOGY-IRI)/$1" \
-	--version-iri "$(config.ONTOLOGY-IRI)/$(TODAY)/$1" \
+	--ontology-iri "$(config.ONTOLOGY_IRI)/$1" \
+	--version-iri "$(config.ONTOLOGY_IRI)/$(TODAY)/$1" \
 	--annotation owl:versionInfo "$(TODAY)" \
 	--output $2
 endef