ZOOMA can be run from the command line, using the "zooma" command. ZOOMA itself takes a single "mode" parameter, and each mode of operation is free to define the parameters they take. Command line help is available...

>: zooma -h
usage: zooma
 -h,--help       Print the help
 -l,--list       List all modes currently configured for ZOOMA
 -text           Run zooma in text mode

For mode specific help, run zooma with a mode option and -mh specified


By default, only "text" mode is available - this mode takes a single text value or a file containing a series of values, and evaluates mappings against either Bioportal and OLS resources, or a supplied ontology. You can see mode-specific help by running a mode with the -mh option:

>: zooma -text -mh
usage: zooma -text [-a | -s] [-d <arg>] [-mh] [-o <arg>]  [-v <arg>]
 -a,--all                      Maps supplied values against terms from a
                               wide variety of ontologies
 -d,--report-directory <arg>   The directory in which reports will be
 -mh,--mode-help               Print the help for the text mode
 -o,--ontology <arg>           The name of the ontology (from the config
                               file) to map against
 -s,--single                   Maps supplied values to a single named
                               ontology (identified in the config file)
 -v,--values <arg>             Path to a file containing the values to map

Within a given mode, there are operations that can be supplied (in the above example, -a and -s). Each operation then has a series of required arguments you may need to supply.

Generally, all the options will be described on the command line by running with the -mh argument.

In this example, I created a file called input.txt which contained one value "thymus". Then I might want to do:

>: zooma -text -s -o efo -v input.txt
Reasoning over
Classifying 2925 elements
Classifying:  100% complete in 00:00:13
Classifying finished in 00:00:13
Checked 1/1 property values.  Estimated time remaining : 0 s.

... and my mappings were written to a report in my current working directory. This report looked like:

Application Name:       ZOOMA (Automatic Ontology Mapper)
Version:        1.0-SNAPSHOT
Run at: 15:57.00, 06.07.10
Run from:       /home/tburdett/zooma
Exit code:      0

thymus  thymus,Thymus gland     Automatic       EFO_0000860