Just upgraded to the current bioconductor (stable) release with org.Mm.eg.db_3.3.0 (and GO.db_3.3.0). It appears that the evidence codes listed in org.Mm.egGO2EG include the code IMR which is not listed at the web site the help for org.Mm.egGO2EG links to. Is this a new code not listed on the GO web site, or is it some kind of a bug/typo? Also, the web link

http://www.geneontology.org/GO.evidence.shtml
given in the help file seems obsolete, it gets redirected to

http://geneontology.org/page/guide-go-evidence-codes

Perhaps that should be changed as well.

Thanks,

Peter

It's not a typo on our side. If you look at AmiGO, and scroll down to negative regulation of macroautophagy, it's listed as IMR. And yes, there is some amount of 'link chasing' needed, as online data do tend to get moved. Unfortunately, during the build process for the annotation packages, which is pretty involved, chasing errant help links tends to get overlooked.

Thanks for the information. For the benefit of people who may find this thread interesting, it turns out that IMR is a synonym for IKR:

ftp://ftp.geneontology.org/pub/go/www/GO.evidence.shtml#ikr

I didn't mean to criticize the maintainers for the link (all the more since the link still works), just suggesting a correction for when the maintainers have a spare minute or two.