goac is a command line tool for counting (user defined) ancestral Gene Ontology (GO) terms in GO term data sets.
goac has been implemented in Java as part of the
forester libraries.
CateGOrizer
is a similar, but web based, application.
Source code is available at [forester] at sourceforge.net
java -cp path\to\forester.jar org.forester.application.goac <file with all GO terms, in 'obo' format> <file with ancestral term ids> <file with go ids to be analyzed>
The <file with all GO terms, in 'obo' format> is a file containing all current GO terms and their relationships. It is available from the Gene Ontology Consortium at ontology file downloads in OBO v1.2 format.
Both the <file with ancestral term ids> and the <file with go ids to be analyzed> contain one GO identifier (e.g. "GO:0003824") per line.
It is acceptable (but not mandatory) to follow GO identifiers with arbitrary text (e.g. "GO:0065007 biological regulation").
'#' is used to indicate a comment (e.g. "# I am a comment").
In order to facilitate batch analyzes, the '>' (greater than) character can be used to denote individual sets in the <file with go ids to be analyzed>.
» example ancestral terms file (top biological process terms)
» example analysis file (with two sets, "first set" and "second set")
» example output
Christian M Zmasek
phylosoft -at- gmail -dot- com
Last updated 2009.04.22
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