PROV - BFO, RO, CCO Mappings

PROV Ontology (PROV-O) is a World Wide Web Consortium (W3C) recommended ontology used to structure data about provenance across a wide variety of domains. Basic Formal Ontology (BFO) is a top-level ontology ISO/IEC standard used to structure a wide variety of ontologies, including the Relation Ontology (RO) and the Common Core Ontologies (CCO). To enhance interoperability between these ontologies, their extensions, and data organized by them, this repo includes a set of mappings that were created according to a criteria and methodology which prioritizes structural and semantic principles.

Usage

PROV-BFO

• PROV-BFO Release version here. This contains only the mapped and extended terms from BFO. Use this file in production.

PROV-RO

• PROV-RO Release version here. This contains only the mapped and extended terms from RO. Use this file in production.

PROV-CCO

• PROV-CCO Release version here. This contains only the mapped and extended terms from CCO. Use this file in production.

Example Usage

1. Import terms from the ontologies that you want to use in your ontology.
2. Import one or more of the mapping files.
3. Use a semantic reasoner or SPARQL queries on your ontology to generate new inferences about data encoded in your ontology.

• See the example ontology demonstrating the first two steps.

Development

• Editor's development version here. This file is used only for development, not intended for production. It contains imports of BFO, CCO, RO, each and all canonical example instances from the PROV-O docs to test with. Open this file in Protege to view the mapping in full context of each aligned ontology. Test this file to ensure consistency among the extensions.

Scope

• Every class and object property from PROV-O and its extensions is mapped to some class or object property from BFO, RO, or CCO.

• The mappings use subsumption and equivalence relations either directly with RDFS and OWL, or indirectly with SWRL rules and property chain axioms. Additional SKOS mappings are provided for extra commentary.

• The following PROV namespaces have been (1) mapped in the mapping files, (2) imported in the editors file, and (3) all Turtle-serialized canonical examples from each have been loaded as instances in the editors file for testing:

  • PROV-O Ontology
  • PROV Access and Query Ontology & Examples
  • PROV Data Dictionary Ontology & Examples
  • PROV Linking Across Provenance Bundles Ontology & Examples
  • PROV Inverses Ontology
    • Automated entailment of mappings for inverse object properties is supported by OWL-DL and OWL-QL. For example, prov:wasMemberOf may be automatically inferred as a subproperty of BFO "part of" because prov:hadMember is a subproperty of BFO "has part" and these PROV terms are inverses of each other.
  • PROV Dublin Core http://www.w3.org/ns/prov-dc# Ontology & Examples

• Bonus mappings between BFO and the SOSA (Sensor, Observation, Sample, and Actuator) ontology are possible, due to the SOSA-PROV Mapping.

Methods

Development Dependencies

• The version of each PROV-O, BFO, RO, and CCO file is specified in the owl:imports of the editor's file prov-mappings-edit.ttl.

• The following W3C semantic web technologies are used to represent the mappings and the mapping criteria:

  • RDF version 1.1, 25 February 2014
  • RDF Schema version 1.1, 25 February 2014
  • OWL version 2, 11 December 2012
  • RDF Turtle version 1.1, 25 February 2014
  • SPARQL version 1.1, 21 March 2013
  • SWRL version, 21 May 2004

• The following tools are used to develop and evaluate the mappings:

  • Protégé version 5.6.3
  • ROBOT version 1.9.5
  • HermiT Reasoner version 1.4.5.456
  • GNU Make version 3.81

Development Process

1. A separate RDF Turtle file is created to extend each ontology with a set of mappings.

2. All mappings and ontologies are imported into the editor's file prov-mappings-edit.ttl to help visualize the mappings using Protege.

   • For testing and reasoning, only terms that are used in a mapping are extracted from RO -- plus their logical dependencies using the MIREOT strategy.
   • The list of RO terms to import is generated in the imports folder.
   • The subset of extracted terms is stored locally and is imported into the editor's file.

3. A mapping file adds triples which relate terms from each ontology using the following "mapping" predicates: rdfs:subClassOf, rdfs:subPropertyOf, owl:equivalentClass, and owl:equivalentProperty.

   • SWRL rules and property chain axioms are used to represent more complex, indirect relations.
   • SKOS relations are used for extra commentary.
   • OWL annotation axioms encode each mapping with justifications as rdfs:comment and other SSSOM metadata.

4. SPARQL queries are used for finding "unmapped" classes and object properties, and also "candidate" superproperties. The HermiT reasoner is used to check consistency and materialize inferences for various development tasks.

5. Mappings for each ontology are encoded as separate extensions to maximize compatibility and minimize dependencies for users, following conventions from the PROV-DC (Dublin Core) mapping.

Testing

• All example instances from the PROV-O documentation and its extensions are temporarily imported into the extended ontology. The HermiT reasoner is used to check if the example instance data is consistent with the extended ontology.

• ROBOT runs HermiT and also SPARQL queries for evaluating the mappings. A SPARQL query that formalizes the mapping criteria is executed to check whether any mappings are missing.

• How to run tests automatically:

  • Push commits to this Github repo, and the Makefile tests will be triggered in Github Workflow files

• How to run tests manually:

  • Requirements: GNU Make
  • Run make from the src directory, or make -C src from this directory
  • Alternatively, run the commands defined within the Makefile.

Release

• Release files are indicated with -directmappings prefix in the file names. These are edited and annotated directly, and imported in the Editor's file for development and testing.
• Turtle (.ttl) versions of the release are currently not built automatically in order to ensure precise formatting, but RDF/XML versions could be automatically built from the Turtle versions.
• Release files do not include imports of the ontologies they map. Why? First, because many terms in the BFO ontologies are not used or relevant to the mappings. Second, because users should not need to import irrelevant terms from any ontology (including PROV ontologies) for their use cases.

Contributors

Tim Prudhomme, Giacomo De Colle, Austin Liebers, Alec Sculley, Karl Xie, Sydney Cohen, and John Beverley

How to cite

Please cite "Mapping PROV-O to BFO" using the DOI https://doi.org/10.5281/zenodo.11338700.