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Update import URIs and versions
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‎README.md

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Tim Prudhomme, Giacomo De Colle, Austin Liebers, Alec Sculley, Karl Xie, Sydney Cohen, and John Beverley
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# How to cite
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Please cite "Mapping PROV-O to BFO" using the DOI https://doi.org/10.5281/zenodo.11338700.
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Please cite "Mapping the Provenance Ontology to Basic Formal Ontology" using the DOI https://doi.org/10.5281/zenodo.11338700.

‎prov-bfo-directmappings.ttl

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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl>
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a owl:Ontology;
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rdfs:label "Basic Formal Ontology (BFO) ISO 21838-2:2020 mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
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owl:versionInfo "2024-06-23"@en ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-10-05> ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
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dc:contributor "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;
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dc:license <https://creativecommons.org/publicdomain/zero/1.0/> ;
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prov:wasDerivedFrom <http://www.w3.org/ns/prov> ,

‎prov-cco-directmappings.ttl

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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl>
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a owl:Ontology;
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rdfs:label "Common Core Ontologies (CCO) mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
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owl:versionInfo "2024-06-23"@en ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-10-05> ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
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owl:imports <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> ;
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rdfs:comment "This mapping depends on the imported PROV-O to BFO mapping" ;
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dc:contributor "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;

‎prov-ro-directmappings.ttl

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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl>
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a owl:Ontology;
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rdfs:label "Relation Ontology (RO) mappings for W3C PROVenance Interchange Ontology (PROV-O)"@en ;
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owl:versionInfo "2024-06-23"@en ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-10-05> ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
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owl:imports <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> ;
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rdfs:comment "This mapping depends on the imported PROV-O to BFO mapping." ;
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dc:contributor "Tim Prudhomme", "Giacomo De Colle" , "Austin Liebers" , "Alec Sculley" , "Peihong Karl Xie", "Sydney Cohen", "John Beverley" ;

‎src/Makefile

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config.EXTRACTED_IMPORTS_NAME := RO-imports-extracted
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EXTRACTED_IMPORTS_FILENAME := $(config.IMPORTS_DIR)/$(config.EXTRACTED_IMPORTS_NAME)
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EXTRACTED_IMPORTS_IRI := https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/$(EXTRACTED_IMPORTS_FILENAME).ttl
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EXTRACTED_IMPORTS_IRI := https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/$(EXTRACTED_IMPORTS_FILENAME).ttl
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IMPORTED_SOURCE_ONTOLOGY := $(config.IMPORTS_DIR)/BFO/ro.owl
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ontology-temp-file := ontology_no_imports.tmp.ttl
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# Extract imported terms from their source ontology to avoid testing with unnecessary axioms
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.PHONY: extract-imports
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extract-imports: $(EXTRACTED_IMPORTS_FILENAME).txt | $(ROBOT_FILE)
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$(ROBOT) extract --input $(IMPORTED_SOURCE_ONTOLOGY) --method subset --term-file $< --output $(EXTRACTED_IMPORTS_FILENAME).ttl;
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$(ROBOT) extract --input $(IMPORTED_SOURCE_ONTOLOGY) --method subset --term-file $< \
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annotate --ontology-iri $(EXTRACTED_IMPORTS_IRI) --output $(EXTRACTED_IMPORTS_FILENAME).ttl;
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# --------------------------------------------------------------------------------

‎src/catalog-v001.xml

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<uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl" uri="../prov-bfo-directmappings.ttl"/>
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<uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl" uri="../prov-ro-directmappings.ttl"/>
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<uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl" uri="../prov-cco-directmappings.ttl"/>
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<!-- Cached ontologies -->
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<!-- <uri name="https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/bfo-core.ttl" uri="imports/BFO/bfo-core.ttl"/> -->
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<uri name="https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/refs/tags/v2.0-2024-11-06/src/cco-merged/CommonCoreOntologiesMerged.ttl" uri="imports/BFO/CommonCoreOntologiesMerged.ttl"/>
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<uri name="https://www.commoncoreontologies.org/2024-11-06/CommonCoreOntologiesMerged" uri="imports/BFO/CommonCoreOntologiesMerged.ttl"/>
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<uri name="http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl" uri="imports/BFO/bfo-core.ttl"/>
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<uri name="https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl" uri="imports/RO-imports-extracted.ttl"/>
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<!-- Other ontologies -->
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<uri name="http://www.w3.org/ns/sosa/prov" uri="imports/SSN/sosa-prov.ttl"/>
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<uri name="http://www.w3.org/ns/sosa/" uri="imports/SSN/sosa.ttl"/>
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<uri name="http://example.org/om-20" uri="examples/om-20.ttl"/>
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<uri name="http://example.org/model" uri="examples/model.ttl"/>
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<uri name="http://maven.renci.org/NeuroBridge/neurobridge" uri="examples/neurobridge_ontology_2023_07_12.owl"/>
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<!-- Examples -->
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<uri name="https://www.w3.org/TR/prov-o/example-1.ttl" uri="examples/example-1.ttl"/>
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<uri name="https://www.w3.org/TR/prov-o/example-2.ttl" uri="examples/example-2.ttl"/>
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<uri name="https://www.w3.org/TR/prov-dictionary/examples.ttl" uri="examples/prov-dictionary-examples.ttl"/>
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<uri name="https://www.w3.org/TR/prov-links/examples.ttl" uri="examples/prov-links-examples.ttl"/>
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<uri name="https://www.w3.org/TR/prov-dc/examples.ttl" uri="examples/prov-dc-examples.ttl"/>
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<uri name="http://example.org/om-20" uri="examples/om-20.ttl"/>
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</catalog>

‎src/imports/RO-imports-extracted.ttl

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@prefix : <http://purl.obolibrary.org/obo/ro.owl#> .
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@prefix : <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl#> .
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@prefix owl: <http://www.w3.org/2002/07/owl#> .
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix xml: <http://www.w3.org/XML/1998/namespace> .
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@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@base <http://purl.obolibrary.org/obo/ro.owl> .
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@base <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl> .
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<http://purl.obolibrary.org/obo/ro.owl> rdf:type owl:Ontology .
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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl> rdf:type owl:Ontology .
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#################################################################
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# Annotation properties
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rdfs:label "causally influenced by" .
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#################################################################
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# Individuals
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#################################################################
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### http://purl.obolibrary.org/obo/RO_0001901
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<http://purl.obolibrary.org/obo/RO_0001901> rdf:type owl:NamedIndividual ;
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<http://purl.obolibrary.org/obo/IAO_0000115> """## Elucidation
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This is used when the statement/axiom is assumed to hold true &apos;eternally&apos;
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## How to interpret (informal)
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First the &quot;atemporal&quot; FOL is derived from the OWL using the standard
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interpretation. This axiom is temporalized by embedding the axiom
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within a for-all-times quantified sentence. The t argument is added to
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all instantiation predicates and predicates that use this relation.
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## Example
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Class: nucleus
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SubClassOf: part_of some cell
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forall t :
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forall n :
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instance_of(n,Nucleus,t)
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implies
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exists c :
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instance_of(c,Cell,t)
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part_of(n,c,t)
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## Notes
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This interpretation is *not* the same as an at-all-times relation""" ;
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rdfs:label "axiom holds for all times"@en .
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### Generated by the OWL API (version 4.5.26) https://github.com/owlcs/owlapi
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### Generated by the OWL API (version 4.5.29) https://github.com/owlcs/owlapi

‎src/imports/RO-imports-extracted.txt

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http://purl.obolibrary.org/obo/RO_0000056
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http://purl.obolibrary.org/obo/RO_0000057
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http://purl.obolibrary.org/obo/RO_0000087
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http://purl.obolibrary.org/obo/RO_0001900
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http://purl.obolibrary.org/obo/RO_0001901
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http://purl.obolibrary.org/obo/RO_0002351
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http://purl.obolibrary.org/obo/RO_0002410
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http://purl.obolibrary.org/obo/RO_0002501

‎src/prov-mappings-edit.ttl

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a owl:Ontology;
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rdfs:label "Editor's file for PROV-BFO Mappings."@en ;
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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 ;
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owl:versionInfo "2024-06-23"@en ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-10-05> ;
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owl:versionIRI <https://github.com/BFO-Mappings/PROV-to-BFO/releases/tag/v2024-11-23> ;
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owl:imports <https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-bfo-directmappings.ttl> , # Release version of PROV-BFO containing actual mappings
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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-ro-directmappings.ttl> , # Release version of PROV-RO containing actual mappings
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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/prov-cco-directmappings.ttl> , # Release version of PROV-CCO containing actual mappings
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<http://www.w3.org/ns/prov-o-inverses>, # PROV Inverses
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<http://www.w3.org/ns/prov-dc>, # PROV Dublin Core
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<https://raw.githubusercontent.com/BFO-ontology/BFO-2020/master/src/owl/bfo-core.ttl>, # BFO Core
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<http://purl.obolibrary.org/obo/bfo/2020/bfo-core.ttl>, # BFO Core
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# <http://purl.obolibrary.org/obo/bfo/2020/bfo.owl> , # BFO temporalized relations
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# <http://purl.obolibrary.org/obo/ro/releases/2024-02-13/ro.owl> , # Don't import all of RO, only import dependent terms below:
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<https://raw.githubusercontent.com/BFO-Mappings/PROV-to-BFO/main/src/imports/RO-imports-extracted.ttl>, # RO imports
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<https://raw.githubusercontent.com/CommonCoreOntology/CommonCoreOntologies/refs/tags/v2.0-2024-11-06/src/cco-merged/CommonCoreOntologiesMerged.ttl>, # CCO
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<https://www.commoncoreontologies.org/2024-11-06/CommonCoreOntologiesMerged> , # CCO
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# Test instances
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<https://www.w3.org/TR/prov-o/example-1.ttl> ,
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# <http://www.w3.org/ns/sosa/prov> ,
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# <http://www.w3.org/ns/sosa/> ,
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# <http://example.org/om-20> ;
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# <http://example.org/model> ;
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# <http://maven.renci.org/NeuroBridge/neurobridge> ;
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.

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