Ontologies are shared in different formats. The default format used by ROBOT is RDF/XML, but there are other OWL formats, RDF formats, and also the OBO file format.
robot convert --input annotated.owl --output results/annotated.obo
The file format is determined by the extension of the output file (e.g.
.obo), but it can also be declared with the
--format option. Valid file formats are:
All ROBOT commands support gzip format files ending with the extension
.gz. Any of the above formats can be compressed as long as the output ends with
.gz (format must be specified for a compressed output):
robot convert --input annotated.owl --format obo \ --output results/annotated.obo.gz
Gzip format files can also be used as input:
robot convert --input annotated.obo.gz \ --output results/annotated.owl
By default, the OBO writer strictly enforces document structure rules. If an ontology violates these, the convert to OBO operation will fail. These checks can be ignored by including
As a document is converted to OBO, you may see
ERROR MASKING ERROR exceptions. This does not indicate failure, but it should be noted that these axioms will not be translated to OBO format. Rather, they will be included in the ontology header under
owl-axioms. See Untranslatable OWL axioms for more details.
You can choose to keep these in the file, or remove them with:
grep -v ^owl-axioms
--check only accepts
false (not case sensitive) as arguments. By default,
--check is true and the OBO document structure checks are performed.
--check is true (which, by default, it is), the document structure rules are strictly enforced. You may choose to review the exception message by running the command again with
--very-very-verbose, or run
convert with the
--check false option to ignore the errors.
Please note that
--check false may result in some unintended output. For example, for terms with more than one definition annotation, a defintion will be chosen at random.
convert requires exactly one
--output. If you do not specify the
--output, or specify more than one, ROBOT cannot proceed. If chaining commands, place
convert command expects either the
--output file name to include an extension, or a format specified by
--output release.owl --format owl --output release