Validating against a upper ontology

Specifying the upper ontology

The upper ontology to check against is specified using either the --upper-ontology <FILE> option (to load it from a local file) or the --upper-ontology-iri <IRI> option (to load it from a resolvable IRI).

Alternatively, the --use-cob true option can be used to automatically load the latest version of the Core Ontology for Biology and Biomedicine, from its standard PURL of http://purl.obolibrary.org/obo/cob.owl.

Alignment with arbitrary root terms

The odk:check-align command can also be used to check alignment against an arbitrary set of root terms, independently of any upper-level ontology.

Root terms to check alignment against can be specified using the --term option (one term per option) or the --term-file option (which expects a path to a file containing one term per line, ignoring blank lines and lines starting with #).

Use the --use-self true to perform a “self-alignment” check: this will use any “preferred root term” self-declared within the ontology itself by means of the IAO:0000700 annotation.

Those options, as well as the options from the previous section, have cumulative effects. For example, the following command:

robot odk:check-align --input uberon.owl \
                      --use-self true \
                      --term UBERON:0000000

will check the alignment of UBERON classes against both its self-declared roots and the additional UBERON:0000000 root. That is, the ontology will be considered “aligned” if all its classes are subclasses of any of the self-declared roots or of UBERON:0000000.

Similarly, with the following command:

robot odk:check-align --input uberon.owl \
                      --use-cob true \
                      --use-self true

the ontology will be considered “aligned” if all its subclasses are subclasses of any of the COB roots or of any of the self-declared roots.

To check that all classes are subclasses of any of the upper ontology roots and additionally that they are also subclasses of any of the self-declared roots, perform the two checks separately:

robot odk:check-align --input uberon.owl \
                      --use-cob true \
      odk:check-align --use-self true

Notes about reasoning

The alignment check requires the use of a reasoner. As with all ROBOT commands that needs a reasoner, you can specify the reasoner to use with the -r, --reasoner option.

Importantly, limitations of the reasoner used may cause some classes to be falsely flagged as non-aligned, if they are logically defined using some class expressions that are not fully supported by the reasoner. To avoid that, if the ontology is known to use class expressions that the reasoner might not support, it is advised to relax the ontology prior to checking its alignment:

robot relax --input uberon.owl \
      odk:check-align --use-cob true

Validation results

By default, the command will fail (forcibly interrupting any pipeline it is a part of in the process) if the ontology is not aligned.

Use the --fail false option to allow the pipeline to continue without erroring out.

If the pipeline continues (either because the ontology is aligned, or because --fail false was used), the next command in the pipeline receives the original, unmodified ontology.

To produce a report from the validation results, use the --report-output <FILE> option. The file will contain a list of all the top-level classes (if any) of the input ontology that are not aligned against the upper ontology.

Restricting the scope of the validation

By default, the command checks the alignment of every single class found in the input ontology.

To only check the alignment of classes in a given namespace, use the --base-iri <NAMESPACE> option – that option may be used repeatedly to check classes in more than one namespace.

For example, to check the alignment of all classes in the OBO UBERON namespace against COB:

robot odk:check-align --input uberon.owl \
                      --base-iri http://purl.obolibrary.org/obo/UBERON_

Furthermore, if the --ignore-dangling true option is used, dangling classes are ignored. In the context of this command, a class is considered “dangling” if the ontology contains no defining axioms (excluding disjointness axioms) and no annotation assertion axioms for the class. You may want to use that option if you are not restricting the alignment check to your ontology’s namespace, to avoid failing the check for any single dangling class that is merely referenced from your ontology. On the other hand, including dangling classes in the check (which is the case by default) could be a way to check that your ontology does not reference dangling classes (which could indicate that you are missing some imports).