Annotate

It’s important to add metadata to an ontology before releasing it, and to update the ontology version IRI.

General annotations can be added one-by-one with --annotation, and the IRIs can be set with --version-iri and --ontology-iri. You can specify as many annotation flags as you’d like in one command:

robot annotate --input edit.owl \
  --ontology-iri "https://github.com/ontodev/robot/examples/annotated.owl" \
  --version-iri "https://github.com/ontodev/robot/examples/annotated-1.owl" \
  --annotation rdfs:comment "Comment" \
  --annotation rdfs:label "Label" \
  --annotation-file annotations.ttl \
  --output results/edi-annotated.owl

Or all at once from a turtle (.ttl) file with --annotation-file:

@prefix rdf:     <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs:    <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl:     <http://www.w3.org/2002/07/owl#> .
@prefix example: <https://github.com/ontodev/robot/examples/> .

example:annotated.owl
  rdf:type owl:Ontology ;
  rdfs:comment "Comment from annotations.ttl file." .

Including at least the following annotations is recommended:

• Ontology & version IRIs
• Title (dcterms:title)
• Description (dcterms:description)
• License (dcterms:license)

If the --interpolate option is used, then some placeholders, of the form %{NAME}, can be used within the annotation values and will be automatically replaced by computed values. Currently supported placeholers are:

• %{ontology_iri}, replaced by the ontology’s IRI;
• %{version_iri}, replaced by the ontology’s version IRI.

Example:

robot annotate --input fbcv-module.owl \
  --interpolate true \
  --link-annotation dc:source %{version_iri} \
  --annotation rdfs:comment "Derived from %{ontology_iri}" \
  --output results/fbcv-annotated.owl

This command can also remove all ontology annotations from your file with --remove-annotations. You can combine this with options to add new annotations:

robot annotate --input annotated.owl \
  --remove-annotations \
  --annotation-file annotations.ttl \
  --output results/annotated_2.owl

Annotating the Source

It’s also possible to annotate the ontology axioms with the ontology IRI 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 annotate –input example2.owl
  –annotate-derived-from true
  –output results/example2_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 annotate –input example2.owl
  –annotate-defined-by true
  –output results/example2_defined_by.owl

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Error Messages

Annotation Format Error

Arguments to --annotation or --axiom-annotation option must follow the PROP VALUE format:

--annotation rdfs:comment "this is a comment"`

Arguments to --link-annotation option must follow the PROP LINK format:

--link-annotation dc:license https://creativecommons.org/publicdomain/zero/1.0/

Arguments to --language-annotation option must follow the PROP VALUE LANG format:

--language-annotation rdfs:label "label" en

Arguments to --typed-annotation option must follow the PROP VALUE TYPE format:

--typed-annotation rdfs:label "label" xsd:string

Missing Annotation Error

No annotations were provided for the annotate command. The --remove-annotations option is also accepted in place of annotations.