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.

The OBO output can be fine-tuned with the --clean-obo option. That option takes a space-separated list of keywords that each enables a customization of the OBO output. Available keywords are:

• drop-extra-labels: forcefully drop supernumerary rdfs:label annotation, to make the ontology compliant with the OBO specification (which dictates that a class can only have one label).
• drop-extra-definitions: likewise, but for IAO:0000115 annotations (definitions).
• drop-extra-comments: likewise, but for rdfs:comment annotations.
• merge-comments: merge rdfs:comment annotations, when there are more than one, into a single annotation (alternative to drop-extra-comments).
• drop-untranslatable-axioms: drop axioms that cannot be represented in OBO format, instead of writing them into the aforementioned owl-axioms header tag.
• drop-gci-axioms: drop axioms that represent General Concept Inclusions, even if they can be legally represented in OBO format.

In addition, the following special keywords are also accepted:

• strict: equivalent to drop-extra-labels drop-extra-definitions drop-extra-comments, to force the production of a valid OBO file by dropping supernumerary annotations as needed.
• true: alias for strict.
• simple: equivalent to strict drop-untranslatable-axioms drop-gci-axioms, to force the production of an OBO file that is not only valid, but also free of any owl-axioms header tag and GCI axioms (which, while perfectly valid with respect to the OBO specification, are not always handled correctly by all OBO parsers).

Examples

Convert a file to OBO and ensure the resulting file is compliant with the OBO specification, dropping supernumerary annotations if necessary:

robot convert -i cl_module.ofn \
  --clean-obo strict \
  --output results/cl_module-strict.obo

Likewise, but with merging comments into a single one instead of dropping the supernumerary comments:

robot convert -i cl_module.ofn \
  --clean-obo "strict merge-comments" \
  --output results/cl_module-strict-mergedcomments.obo

Convert a file to a simple variant of the OBO format (without any owl-axioms tag and GCI axioms):

robot convert -i cl_module.ofn \
  --clean-obo simple \
  --output results/cl_module-simple.obo

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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