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:

• json - OBO Graphs JSON
• obo - OBO Format
• ofn - OWL Functional
• omn - Manchester
• owl - RDF/XML
• owx - OWL/XML
• ttl - Turtle

In the following example we convert an input ontology to OBOGraphs JSON, explicitly specifying the target format with --format:

robot convert -i ro-base.owl --format json -o results/ro-base.json

Handling Compressed Files

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

Converting to OBO Format

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

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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.

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