There is an updated version (3.11.4) of GO.db and the org packages available. This new version of GO.db utilizes the new OBO file format we have been working on. There are some really big changes in this version of GO.db that we wanted the community to be aware of.
The GO Consortium has made changes to the directed acyclic graph (DAG) such as removing 'cell part'. 'cell part' is the only child of the 'cell' term and had lots of children. 'cell' is at the very top of the CC DAG, right below 'cellular component'. When doing the following query on the newer org.Hs.eg.db package:
dbGetQuery(con, “select count() from go_cc_all where go_id=‘GO:0005623’;“)
we see a drastic decrease in the number of genes annotated to 'cell' as compared to the previous version (3.11.1). This also results in no offspring since they removed 'cell part'. Cross-checking this information with AmiGO it seems that the GO Consortium simply pruned out a huge part of the CC DAG. This may influence many packages which is why we wanted to bring to the community's attention.
Please let us know if you have any questions and thank you again for your patience as we made this file format transition.