Bumping for interest. I also have the impression that most tutorials and manuals treat this use-case very poorly if at all. For example for Bioconductor packages most seem to rely on a list of geneids to either download the annotation or use an existing BioC annotation package. It even seems very hard to determine if a package can deal with self defined term annotations at all. Possibly we should have a list of BioC packages that can.

I found this https://stat.ethz.ch/pipermail/bioconductor/2011-February/037834.html as a thread on the BioC mailing list, but it doesn't look straight-forward to extract the required steps. I suggest that the documentation of most such packages could use some improvement.