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PROV

README.md

PROV - BFO Extension

Contributors

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

Usage

Development

  • Editor's development version here. This contains imports of BFO, CCO, RO, and 91 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.

PROV-BFO

PROV-RO

PROV-CCO

Scope

  • The mapping goal is to subsume every PROV-O term under some BFO (Basic Formal Ontology) or RO (Relation Ontology) term. A separate extension which maps PROV-O to CCO (Common Core Ontologies) is also proposed.

  • This mapping aligns PROV-O to these top-level ontologies to promote interoperability between PROV-O users and BFO users.

  • At the same time, the mapping is encoded as an extension to maximize compatibility and minimize dependencies for existing PROV-O users.

  • The mapping follows conventions from the PROV-DC (Dublin Core) mapping by serializing as an RDF Turtle extension of PROV.

  • Further BFO interpretations of PROV-O are also offered:

    • An extension of prov:Agent using a new anonymous instance of BFO "role", which is realized by an instance of prov:Activity.
    • An extension of prov:StartedAtTime and prov:EndedAtTime in terms of BFO "temporal region".

  • The following PROV namespaces have been (1) mapped in the mapping files, (2) imported in the editors file, and (3) all Turtle-serialized 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

Methods

Development

  1. A new PROV-BFO extension ontology is created.
  2. BFO and RO are temporarily imported into PROV-BFO to help visualize the mappings in the class hierarchy using Protege
    • For testing and reasoning, only terms we use are extracted from RO -- plus their logical dependencies using the MIREOT strategy with OntoFox.
    • The list of RO terms to import is specified in the OntoFox_inputs folder.
    • The subset of RO extracted from OntoFox is stored locally in the OntoFox_outputs folder. This subset is imported into the editor's version of the mapping.
  3. SPARQL queries are used for finding unsubsumed classes and object properties, and also "candidate" superproperties.
  4. PROV-BFO adds triples which relate terms from each ontology using the following "mapping" predicates: rdfs:subClassOf, rdfs:subPropertyOf, and owl:equivalentClass, similar to the PROV-DC extension.
  • (Previously, the alignment mappings were added directly to a new version of PROV. These are kept in this folder for historical documentation but should not be used.)

Metadata

  • The mappings should include the following metadata:
    • A justification for each mapping
    • A confidence score for each mapping
  • This metadata could be specified either with some standardized annotation properties or an SSSOM template
  • The SSSOM template is generated from the mapping file using a SPARQL query and the Makefile

Testing

  • 91 example instances from the PROV-O documentation 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

  • 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 PROV directory, or make -C PROV from the BFO-Mappings directory

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 not currently automatically built in order to ensure precise formatting, but RDF/XML versions could be automatically built from the Turtle versions.