obo2obo

The obo2obo utility loads one or more obo files, optionally filters them, and then saves the results into one or more new obo files.

obo2obo [-formatversion <myversion>] [-parsecomments] [-writecomments] \

   [-script <scriptname> [<arg1> <arg2> ... <argN>] \;] \

   <inputfile1> <inputfile2> ... <inputfileN> -o <outputspec1> -o <outputspec2> -o <outputspecN>

or

obo2obo -?

The command line parameters are:

At least one input file and one output specification are required. By default, obo2obo writes out OBO 1.2 format.

Output Specification

The output specification gives an output file name, and may optionally specify some options for writing the file. The output spec format is:

-o [-f <filterfile.xml>] [-allowdangling] [-p <prefilter property id>] [-strictrootdetection]
[-saveimpliedlinks|-saveallimpliedlinks] [-realizeimpliedlinks]
<outputfile.obo>

The command line parameters are:

Also see Java Options on the Command-line

Example:

To convert an OBO 1.2 file at ~/cvs/go/ontology/gene_ontology.obo into an OBO 1.0 file:

obo2obo -formatversion OBO_1_0 ~/cvs/go/ontology/gene_ontology.obo -o ~/cvs/go/ontology/gene_ontology_1.0.obo

To filter ~/cvs/go/ontology/gene_ontology.obo using the filter yeast_goslim_filter.xml to generate a file in OBO 1.0 format:

obo2obo -formatversion OBO_1_0 ~/cvs/go/ontology/gene_ontology.obo -o -f yeast_goslim_filter.xml ~/cvs/gso/ontology/goslim_yeast_1.0.obo