README.md

rdf-expressionizer

Translates named classes to equivalent class expressions.

The primary use case for this is rewiring ontologies that use upper ontologies such as BFO, preserving semantic entailment, and hiding upper ontology classes in an orthogonal hierarchy.

Installation

pipx install rdf-expressionizer
rdf-expressionizer --help

Example Workflows

Rewiring an ontology that uses BFO

rdf-expressionizer replace -m bfo_xbfo_mappings ro.owl -o ro-rewired.owl

Note that the semantics of axioms are preserved, but structurally rewritten.

For example, the following axiom:

• occurs in Domain occurrent nature

Is rewritten to:

• occurs in Domain has characteristic some occurrent nature

TODO: decide on which ObjectProperty to use for bfo_xbfo_mappings

Note the resulting ontology has dangling flat label-less classes. These are semantically correct, but to give them labels and hierarchy, merge with XBFO.

robot merge -i ro-rewired.owl -i src/rdf-expressionizer/xbfo.owl -o ro-rewired-pretty.owl

Rewiring an ontology preserving COB subset

rdf-expressionizer replace -x COB -m bfo_xbfo_mappings ro.owl -o ro-rewired.owl

This excludes (-x or --exclude-subset) the COB subset of BFO from the rewiring.

Augmenting COB with equivalence axioms

rdf-expressionizer augment  -m bfo_xbfo_mappings cob.owl -o cob-augmented.owl

Testing

git clone <this repo>
poetry install
make test

This runs internal unit tests, and additional tests.

One of the tests does the following:

• injects an invalid axiom into RO
  • Cell occurs-in some 'Multi-cellular organism'
  • this axiom is designed to cause incoherency when combined with upper level BFO disjointness axioms
• creates a rewired version of RO
• runs robot explain
• checks the intended unsatisfiable axiom is detected

• cell SubClassOf Nothing ##

  • cell SubClassOf anatomical structure
    • anatomical structure SubClassOf material anatomical entity
      • material anatomical entity SubClassOf anatomical entity
        • anatomical entity SubClassOf has characteristic some independent continuant nature
          • independent continuant nature SubClassOf continuant nature
  • cell SubClassOf occurs in some multicellular anatomical structure
    • occurs in Domain has characteristic some occurrent nature
  • has characteristic some continuant nature DisjointWith has characteristic some occurrent nature

Limitations

• Ontology must be in RDF serialization
  • TODO: add options for non RDF/XML serializations