I am building the annotation db0 packages for the upcoming Bioconductor release, which are used to generate all the orgDb and chip annotation packages that we distribute. Up to the previous release we have always included IPI identifiers (as part of the table containing the PROSITE and PFAM IDs). Unfortunately, IPI is no longer maintained (since 2011), and UniProt, which is where we got data for the last few releases, has now dropped support as well.
Given that this annotation source is no longer maintained, I decided to exclude these IDs from the current build of the following db0 packages:
In addition, it is not clear to me (nor can Marc recall) where the data for PFAM in the yeast.db0 package comes from. Given that we are pretty far behind schedule for these packages, I have excluded that table as well.
If this will break anybody's package, or if there are people who rely on these IDs, I can just parse out of the last release and deprecate, so you will have the IDs for one more release. However, if nobody cares about such things, I will just go with what we have. Please speak up if this will affect you.