Merge pull request #30 from BFO-Mappings/conservativity

Conservativity verification

.gitignore

@@ -4,5 +4,8 @@
 # This is where Makefile artifacts and dependencies go
 build/lib
 
+old-prov-triples.ttl
+new-prov-triples.ttl
+
 # Ontop files
 *.properties

prov-bfo-directmappings.ttl

@@ -11,8 +11,8 @@
 <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:versionInfo       "2024-05-27"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-05-27> ;
+  owl:versionInfo       "2024-06-23"@en ;
+  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-06-23> ;
   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> ,

prov-cco-directmappings.ttl

@@ -13,8 +13,8 @@
 <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:versionInfo       "2024-05-27"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-05-27> ;
+  owl:versionInfo       "2024-06-23"@en ;
+  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-06-23> ;
   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" ;
   dc:contributor        "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;
@@ -265,15 +265,6 @@ prov:pairKey rdf:type owl:ObjectProperty .
     rdfs:comment  "A Key-Entity Pair is about a key because Key-Entity Pairs are Information Content Entities"@en .
 
 
-prov:insertedKeyEntityPair rdf:type owl:ObjectProperty .
-[]  rdf:type owl:Axiom ;
-    owl:annotatedSource   prov:insertedKeyEntityPair ;
-    owl:annotatedProperty rdfs:subPropertyOf ;
-    owl:annotatedTarget   cco:has_output ;
-    sssom:object_label    "has output" ;
-    rdfs:comment  "Insertion of a Key-Entity Pair has output that Key-Entity Pair"@en .
-
-
 # PROV-AQ object property mappings
 prov:has_anchor rdf:type owl:ObjectProperty .
 []  rdf:type owl:Axiom ;
@@ -518,4 +509,34 @@ prov:qualifiedInvalidation rdf:type owl:ObjectProperty .
                             ] ;
                 rdf:rest rdf:nil
                 ]
+ ] .
+
+
+# prov:insertedKeyEntityPair(?x,?y) ^ obo:BFO_0000015(?x) -> cco:has_output(?x,?y)
+[ <http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled> "true"^^xsd:boolean ;
+   rdfs:comment "If the Insertion of a Key-Entity Pair is a process, then that Insertion has output that Key-Entity Pair"@en ;
+   rdfs:label "Insertion insertedKeyEntityPair -> has_output" ;
+   rdf:type swrl:Imp ;
+   swrl:body [  rdf:type swrl:AtomList ;
+                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
+                            swrl:propertyPredicate prov:insertedKeyEntityPair ;
+                            swrl:argument1 :x ;
+                            swrl:argument2 :y
+                            ] ;
+                rdf:rest [ rdf:type swrl:AtomList ;
+                            rdf:first [ rdf:type swrl:ClassAtom ;
+                                        swrl:classPredicate obo:BFO_0000015 ;
+                                        swrl:argument1 :x
+                                    ] ;
+                            rdf:rest rdf:nil
+                        ]
+                ] ;
+   swrl:head [  rdf:type swrl:AtomList ;
+                rdf:first [ rdf:type swrl:IndividualPropertyAtom ;
+                            swrl:propertyPredicate cco:has_output ;
+                            swrl:argument1 :x ;
+                            swrl:argument2 :y
+                            ] ;
+                rdf:rest rdf:nil
+                ]
  ] .

prov-ro-directmappings.ttl

@@ -11,8 +11,8 @@
 <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:versionInfo       "2024-05-27"@en ;
-  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-05-27> ;
+  owl:versionInfo       "2024-06-23"@en ;
+  owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-06-23> ;
   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." ;
   dc:contributor        "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;

src/Makefile

@@ -17,13 +17,14 @@ config.DEV_IRI			:= $(config.ONTOLOGY-IRI)/dev
 config.MODULES_IRI		:= $(config.DEV_IRI)/modules
 
 # Local project directories
-config.SOURCE_DIR		:= /
-config.TEMP_DIR			:= build/artifacts
-config.RELEASE_DIR		:= /
-config.REPORTS_DIR		:= $(config.TEMP_DIR)
-config.QUERIES_DIR		:= sparql
-config.IMPORTS_DIR		:= imports
-config.LIBRARY_DIR		:= ../build/lib
+config.SOURCE_DIR				:= /
+config.TEMP_DIR					:= build/artifacts
+config.RELEASE_DIR				:= /
+config.REPORTS_DIR				:= $(config.TEMP_DIR)
+config.QUERIES_DIR				:= sparql
+config.CONSTRUCT_QUERIES_DIR	:= sparql/construct
+config.IMPORTS_DIR				:= imports
+config.LIBRARY_DIR				:= ../build/lib
 
 # Settings
 # These will cause targets run by a Github Action to fail, if desired
@@ -61,6 +62,9 @@ candidates-complex:
 	$(ROBOT) query --input $(EDITOR_BUILD_FILE) -q $(config.QUERIES_DIR)/candidate-superproperties-complex.rq $(config.TEMP_DIR)/candidate-superproperties-complex.tsv --use-graphs true ;
 
 
+# Axioms to materialize in reasoning
+AXIOM_GENERATORS = "SubClass EquivalentClass SubObjectProperty EquivalentObjectProperty InverseObjectProperties"
+
 # Check for unmapped terms after materializing inferred mappings (after removing individuals)
 unmapped:
 	$(ROBOT) remove --input $(EDITOR_BUILD_FILE) --select individuals \
@@ -70,9 +74,19 @@ unmapped:
 # Materialize all mappings as a list
 inferred-mappings:
 	$(ROBOT) remove --input $(EDITOR_BUILD_FILE) --select individuals \
-	reason --reasoner HermiT --axiom-generators "SubClass SubObjectProperty InverseObjectProperties" --include-indirect true \
+	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
 
+# 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 \
+	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 \
+	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
+
 
 # Remove CCO individuals to speed up reasoner
 config.CCO_FILENAME = ../MergedAllCoreOntology-v1.4-2023-04-07

src/build/artifacts/deductive-diff.txt

@@ -0,0 +1 @@
+Ontologies are identical

src/build/artifacts/inferred-mappings.csv

@@ -10,7 +10,6 @@ End,http://www.w3.org/2000/01/rdf-schema#subClassOf,process boundary
 Entity,http://www.w3.org/2000/01/rdf-schema#subClassOf,continuant
 Generation,http://www.w3.org/2000/01/rdf-schema#subClassOf,process boundary
 Influence,http://www.w3.org/2000/01/rdf-schema#subClassOf,occurrent
-Insertion,http://www.w3.org/2000/01/rdf-schema#subClassOf,process
 InstantaneousEvent,http://www.w3.org/2000/01/rdf-schema#subClassOf,occurrent
 Invalidation,http://www.w3.org/2000/01/rdf-schema#subClassOf,process boundary
 Key-Entity Pair,http://www.w3.org/2000/01/rdf-schema#subClassOf,generically dependent continuant
@@ -24,7 +23,6 @@ Person,http://www.w3.org/2000/01/rdf-schema#subClassOf,Person
 Plan,http://www.w3.org/2000/01/rdf-schema#subClassOf,generically dependent continuant
 Plan,http://www.w3.org/2000/01/rdf-schema#subClassOf,Information Content Entity
 Publish,http://www.w3.org/2000/01/rdf-schema#subClassOf,process
-Removal,http://www.w3.org/2000/01/rdf-schema#subClassOf,process
 Replace,http://www.w3.org/2000/01/rdf-schema#subClassOf,process
 RightsAssignment,http://www.w3.org/2000/01/rdf-schema#subClassOf,process
 Role,http://www.w3.org/2000/01/rdf-schema#subClassOf,role
@@ -84,8 +82,6 @@ has_provenance,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,is subject of
 influenced,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,causally related to
 influencer,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,causally related to
 informed,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,causally related to
-insertedKeyEntityPair,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,has participant
-insertedKeyEntityPair,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,has output
 invalidated,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,has participant
 invalidated,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,has participant
 invalidated,http://www.w3.org/2000/01/rdf-schema#subPropertyOf,has participant

src/catalog-v001.xml

@@ -5,7 +5,7 @@
     <uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl" uri="../prov-ro-directmappings.ttl"/>
     <uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl" uri="../prov-cco-directmappings.ttl"/>
     <!-- Cached ontologies -->
-    <uri name="https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/bfo-core.ttl" uri="imports/BFO/bfo-core.ttl"/>
+    <!-- <uri name="https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/bfo-core.ttl" uri="imports/BFO/bfo-core.ttl"/> -->
     <uri name="https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/master/cco-merged/MergedAllCoreOntology-v1.5-2024-02-14.ttl" uri="imports/BFO/MergedAllCoreOntology-v1.5-2024-02-14.ttl"/>
     <uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl" uri="imports/RO-imports-extracted.ttl"/>
     <!-- Other ontologies -->

src/imports/BFO/bfo-ontologies.ttl

@@ -0,0 +1,16 @@
+@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix owl:  <http://www.w3.org/2002/07/owl#> .
+@base <bfo-ontologies.ttl> .
+
+<bfo-ontologies.ttl>
+   a owl:Ontology;
+   rdfs:comment "This file is used for analytics only"@en ;
+   owl:imports <https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/bfo-core.ttl>, # BFO Core
+               # <http://purl.obolibrary.org/obo/bfo/2020/bfo.owl> , # BFO temporalized relations
+
+               # <http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.owl> , # Don't import all of RO, only import dependent terms below:
+               <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl>, # RO imports
+
+               <https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/master/cco-merged/MergedAllCoreOntology-v1.5-2024-02-14.ttl>, # CCO
+.

src/prov-mappings-edit.ttl

@@ -10,8 +10,8 @@
    a owl:Ontology;
    rdfs:label "Editor's file for PROV-BFO Mappings."@en ;
    rdfs:comment "Open this in Protege to view the full mapping in context. Test the mapping with the imports in this file. This keeps imports out of the release version."@en ;
-   owl:versionInfo       "2024-05-27"@en ;
-   owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-05-27> ;
+   owl:versionInfo       "2024-06-23"@en ;
+   owl:versionIRI        <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-06-23> ;
    owl:imports <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> , # Release version of PROV-BFO containing actual mappings
                <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl> , # Release version of PROV-RO containing actual mappings
                <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl> , # Release version of PROV-CCO containing actual mappings

src/sparql/constructs/prov-triples.rq

@@ -0,0 +1,18 @@
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX swrl: <http://www.w3.org/2003/11/swrl#> 
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+
+PREFIX prov: <http://www.w3.org/ns/prov#>
+PREFIX bfo: <http://purl.obolibrary.org/obo/BFO_>
+
+CONSTRUCT { 
+  ?targetTerm ?predicate ?sourceTerm
+} WHERE {
+    FILTER ( 
+      STRSTARTS(STR(?targetTerm), STR(prov:)) &&
+      STRSTARTS(STR(?sourceTerm), STR(prov:))
+    )
+    ?targetTerm ?predicate ?sourceTerm . 
+}

src/sparql/inferred-mappings.rq

@@ -10,7 +10,7 @@ PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
 PREFIX cco: <http://www.ontologyrepository.com/CommonCoreOntologies/>
 
 # Note: filters only work when all referenced terms and their axioms are succesfully imported
-# Note: this should be used after materializing all mappings, however this query does not necessarily show all mappings
+# Note: this should be used after materializing all mappings, however this query does not necessarily show all mappings (ex. SWRL rules)
 SELECT ?targetTermLabel ?predicate ?sourceTermLabel
 WHERE {
     VALUES ?termType { owl:Class owl:ObjectProperty  } .