Merge

OWL ontologies are often divided into several .owl files, with owl:imports statements to bring them together. Sometimes you want to take all those imports and merge them into a single ontology with a single .owl file. This can be chained with annotate to specify an IRI for the output ontology.

robot merge --input edit.owl \
annotate --ontology-iri https://github.com/ontodev/robot/examples/merged.owl\
 --output results/merged.owl

You don’t need owl:import statements: you can merge any number of ontologies by using multiple --input arguments. All the ontologies and their imports are merged into the first ontology.

robot merge --input edit.owl --input edit2.owl --output results/merged2.owl

You can also specify merging of multiple files that match a pattern with --inputs. The argument to --inputs must be a quoted wildcard pattern. This option supports ? to match any single character, or * to match any number of characters.

This command will merge edit.owl and edit2.owl:

robot merge --inputs "edit*.owl" --output results/merged2.owl

A merge can be ‘undone’ with unmerge.

Import Closure

The --collapse-import-closure option is, by default, true. As shown in the first example above, running merge on an ontology with owl:imports statements will merge these into a single file. The owl:imports statements are also removed from the ontology.

By adding --collapse-import-closure false, the imports will not be merged in and the owl:imports statements will remain.

Ontology Annotations

The --include-annotations option is, by default, false. This refers to the ontology annotations, and when merging, these are typically ignored and the output will only include the ontology annotations from the first input.

If you would like to merge the ontology annotations from several inputs, add --include-annotations true.

Provenance Annotations

It’s also possible to annotate the imported or merged ontology axioms with the source ontology or version IRI.

• --annotate-derived-from true: annotates all axioms with the source’s version IRI if it exists, else with the ontology IRI, using prov:wasDerivedFrom. If the axiom already has an annotation using this property (prov:wasDerivedFrom), the existing annotation will be kept and no new annotation will be added.

  robot merge –catalog catalog.xml
  –input imports-nucleus.owl
  –annotate-derived-from true
  –output results/merged_derived_from.owl

• --annotate-defined-by true: annotates all entities (class, data, annotation, object property and named individual declaration axioms) with the source’s IRI using rdfs:isDefinedBy. If the term already has an annotation using this property (rdfs:isDefinedBy), the existing annotation will be kept and no new annotation will be added.

  robot merge –input example2.owl –input merge.owl
  –annotate-defined-by true
  –output results/merged_defined_by.owl

--annotate-defined-by excludes entities from the reserved OWL 2 vocabularies (RDF, RDFS, XSD and OWL).