ROBOT

- - - - - - - - - -
view on github
usage
common errors
chaining commands
prefixes
makefile
- - - - - - - - - -
annotate
convert
diff
extract
filter
materialize
merge
mirror
query
reason
reduce
relax
repair
report
template
unmerge
validate
verify
- - - - - - - - - -

Prefixes

Terms in OBO and OWL are identified using IRIs (Internationalized Resource Identifiers), which generalize the familiar addresses for web pages. IRIs have many advantages, but one of their disadvantages is that they can be pretty long. So we have standard ways to abbreviate IRIs in a particular context by specifying prefixes. For example, Turtle files start with @prefix statements, SPARQL queries start with PREFIX statements, and JSON-LD data includes a @context with prefixes.

For robot we use the JSON-LD format. See obo_context.jsonld for the JSON-LD context that is used by default. It includes common, general linked-data prefixes, and prefixes for all the OBO library projects.

If you do not want to use the defaults, you can use the --noprefixes option. If you want to replace the defaults, use the --prefixes option and specify your JSON-LD file. Whatever your choice, you can add more prefixes using the --prefix option, as many times as you like. Finally, you can print or save the current prefixes using the export-prefixes command. Here are some examples:

robot --noprefixes --prefix "foo: http://foo#" \
  export-prefixes --output results/foo.json

robot --prefixes foo.json -p "bar: http://bar#" -p "baz: http://baz#" \
  export-prefixes

The various prefix options can be used with any command. When chaining commands, you usually want to specify all the prefix options first, so that they are used “globally” by all commands. But you can also use prefix options for single commands. Here’s a silly example with a global prefix “foo” and a local prefix “bar”. The first export includes both the global and local prefixes, while the second export includes only the global prefix.

robot --noprefixes --prefix "foo: http://foo#" \
  export-prefixes --prefix "bar: http://bar#" \
  export-prefixes

Error Messages

JDON-LD Error

ROBOT encounterd a problem while writing the given prefixes to JSON-LD.