gosim

Calculates networks of semantic similarity scores using the Gene Ontology as proposed in Schlicker et al., 2006.

Gene ontology score networks can get very large, consider using a cutoff value (parameter -c). The calculation of a network may take some time depending on the power of the computer you use.

Call the tool without any command line arguments to get detailed information about the parameters for this program.

See also:

Example calls

Note: The GO ontology and annotation files are only provided with this package for yeast. The corresponding files for other species or updated versions for yeast can be downloaded from the Gene Ontology website.
cmdline.sh gosim -gonet data/go/gene_ontology_edit.obo -name bp -anno data/go/gene_association.sgd

cmdline.sh gosim -gonet data/go/gene_ontology_edit.obo -name mf -anno data/go/gene_association.sgd -rel isa -termsim resnik -funsim colrowavg -c 3.0 -o go.net -oz


Important note: The protein identifier types used in the GO files might not be the same as in the other data files. You might have to use a name mapping file. ProCope provides such a name mapping file for yeast in data/yeastmappings_YYMMDD.txt.
Command line option: -namemap data/yeastmappings_YYMMDD.txt



ProCope documentation