ROBOT is a command-line tool and library for automating ontology development tasks, with a focus on Open Biological and Biomedical Ontologies (OBO). It can be used as a command-line tool or as a library for any language on the Java Virtual Machine.

References:

• R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton
  ROBOT: A tool for automating ontology workflows,
  BMC Bioinformatics, vol. 20, July 2019.

• ROBOT GitHub page
• ROBOT Home page

• Module Name: robot (see the modules page for more information)
• Unusual environment variables set
  • ROBOT_HOME  installation directory
  • ROBOT_BIN       executable directory
  • ROBOT_SRC       source code directory
  • ROBOT_DATA  sample data directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=4g
[user@cn0911 ~]$module load robot   
[+] Loading singularity  3.10.5  on cn0833
[+] Loading robot  1.9.4
[user@cn0911 ~]$robot
usage: robot [command] [options] 
    --add-prefix       add prefix 'foo: http://bar' to the output
    --add-prefixes     add JSON-LD prefixes to the output
    --catalog          use catalog from provided file
 -h,--help                  print usage information
    --noprefixes            do not use default prefixes
 -p,--prefix           add a prefix 'foo: http://bar'
 -P,--prefixes         use prefixes from JSON-LD file
    --strict                use strict parsing when loading an ontology
 -V,--version               print version information
 -v,--verbose               increased logging
 -vv,--very-verbose         high logging
 -vvv,--very-very-verbose   maximum logging, including stack traces
 -x,--xml-entities          use entity substitution with ontology XML
                            output
commands:
 help             print help for command
 annotate         annotate ontology
 collapse         minimize an ontology based on a threshold
 convert          convert ontology
 diff             find the differences between two ontologies
 expand           expand ontology
 explain          explain derivation of an inferred axiom
 export           export ontology as a table
 export-prefixes  export prefixes to a file
 extract          extract terms from an ontology
 filter           filter ontology axioms
 materialize      materialize ontology
 measure          compute the metrics of an ontology
 merge            merge ontologies
 mirror           mirror ontology imports closure
 python           start a server to run ROBOT with Py4J
 query            query an ontology
 reason           reason ontology
 reduce           reduce ontology
 relax            relax ontology
 remove           remove axioms from an ontology
 rename           rename entities based on given mappings
 repair           repair terms from an ontology
 report           report terms from an ontology
 template         build an ontology from a template
 unmerge          unmerge ontologies
 validate-profile validate ontology against an OWL profile
 verify           verify an ontology does not violate rules (as queries)
[user@cn0911 ~]$robot -h
usage: robot [command] [options] 
    --add-prefix       add prefix 'foo: http://bar' to the output
    --add-prefixes     add JSON-LD prefixes to the output
    --catalog          use catalog from provided file
 -h,--help                  print usage information
    --noprefixes            do not use default prefixes
 -p,--prefix           add a prefix 'foo: http://bar'
 -P,--prefixes         use prefixes from JSON-LD file
    --strict                use strict parsing when loading an ontology
 -V,--version               print version information
 -v,--verbose               increased logging
 -vv,--very-verbose         high logging
 -vvv,--very-very-verbose   maximum logging, including stack traces
 -x,--xml-entities          use entity substitution with ontology XML
                            output

[user@cn0911 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$