Normalizing an ontology

The odk:normalize command is intended to perform various “normalisation” operations.

By default, the command does nothing. Each of the normalisation operations described below must be explicitly enabled with its corresponding option.

The special flag --all enables all the available normalisation operations. When it is used, a particular operation can still be disabled by explicitly using the corresponding option with a false argument. For example, to perform all possible normalisations operations except the merging of duplicated axioms:

robot odk:normalize --all --merge-axioms false

Injecting declarations for subset properties

This is requested with the --subset-decls true option.

When enabled, if the ontology contains any annotation using the oboInOwl:inSubset property (which is used, across OBO ontologies, to mark a class as belonging to a given subset), and the annotation value is an IRI, this command will inject an axiom declaring that the IRI represents a subproperty of oboInOwl:SubsetProperty.

The command will only consider IRIs that fall under the following namespaces:

http://purl.obolibrary.org/obo/;
http://www.ebi.ac.uk/efo/;
http://w3id.org/biolink/.

Additional namespaces can be specified using the --base-iri <NAMESPACE> option.

Injecting declarations for synonym type properties

This is requested using the --synonym-decls true option.

When enabled, this performs a task similar to --subset-decls true, but for properties that represent synonym types. That is, if the ontology contains any annotation using the oboInOwl:hasSynonymType property (used on synonym annotations to indicate the nature of the synonym, e.g. abbreviations, etc) and the annotation is an IRI, the command will inject an axiom declaring that the IRI represents a subproperty of oboInOwl:SynonymTypeProperty.

The command will consider IRIs that fall under the namespaces listed in the previous section. Additional namespaces can be specified using the --base-iri <NAMESPACE> option.

(The --base-iri option thus affects both the --subset-decls and the --synonym-decls features. If you want to use different namespaces for each operation, you must invoke the odk:normalize command twice, one time to inject subset declarations, and a second time to inject synonym type declarations.)

Merging duplicated axioms

This is requested using the --merge-axioms true option.

When enabled, this will merge duplicated axioms that differ only by their annotations. For example, if the ontology contains the following axioms:

SubClassOf(UBERON:1234 UBERON:5678)
SubClassOf(Annotation(oboInOwl:hasDbXref "PMID:9999") UBERON:1234 UBERON:5678)
SubClassOf(Annotation(rdfs:comment "To be checked") UBERON:1234 UBERON:5678)

they will be replaced by a single axiom as follows:

SubClassOf(Annotation(oboInOwl:hasDbXref "PMID:9999")
           Annotation(rdfs:comment "To be checked")
           UBERON:1234 UBERON:5678)

That option is a (hopefully) temporary workaround until the corresponding feature in ROBOT (robot repair --merge-axiom-annotations true) is fixed, as it does not currently (as of ROBOT 1.9.7) work as expected.

Injecting a dc:source annotation

This is requested using the add-source option.

When enabled, this will inject a dc:source annotation ontology, set from the version IRI of the input ontology. This is used in the ODK to annotate import modules with the version IRI of the upstream ontology they are derived from.

(It is hoped that this could soon be replaced by a built-in feature in ROBOT’s annotate command.)