ROBOT

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getting started
common errors
chaining commands
global options
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annotate
convert
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ROBOT is licensed under the
BSD 3-Clause License.
Theme by orderedlist

Convert

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:

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 --check false.

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

Error Messages

Check Arg Error

--check only accepts true or false (not case sensitive) as arguments. By default, --check is true and the OBO document structure checks are performed.

OBO Structure Error

If --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.

Output Error

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 last.

Format Error

The convert command expects either the --output file name to include an extension, or a format specified by --format.

Correct:

--output release.owl
--format owl --output release

Incorrect:

--output release