To map a set of annotations to high level GO terms (GO slim) you use the Map2Slim option in OWLTools.
Given a GO slim file, and a current ontology (in one or more files), the Map2Slim script will map a gene association file (containing annotations to the full GO) to the terms in the GO slim. This script is an option of OWLTools, and it can be used to either create a new gene association file, which contains the most pertinent GO slim accessions, or in count-mode, in which case it will give distinct gene product counts for each slim term.
Background information and details on how to download, install, and implement OWLTools, as well as instructions on how to run the Map2Slim script are available from the OWLTools Wiki at https://github.com/owlcollab/owltools/wiki/Map2Slim.
Details on the GO Slim and the GO Prokaryotic Subset are available from our documentation pages.
Additional details about the GO database and how to query it are available from our documentation pages at the legacy database guide.