Hi Jim, You asked me on Friday where the PFAM Ids for yeast came from and I couldn't recall because at the moment I was at Seattle Childrens (and thus nowhere near my copy of my source code). But I also said I would look into it for you later (and I have). Here is what my code tells me: So ever since IPI shut down, we have been getting the PFAM and IPI data from UniProt. There is a script in the UniProt.ws package called processDataForBuild.R that is supposed to be called by the script "src_build.sh" (it's the last thing that script does). That code should get the pfam data from yeast for you. Please note that yeast required a lot of special code to get it processed. Nothing with yeast annotations is ever easy. It's like karmic accounting to compensate for all the bread and beer. ;)
Let me know if you need any more explanations about what is in there. Because of the crazy timing, before I left I build I pushed into devel a fresh set of .DB0s and core packages (in late August) just in case it was too crazy to do a refresh right now. But it sounds like you won't need that. Marc On Sun, Oct 4, 2015 at 6:27 AM, James W. MacDonald <jmac...@uw.edu> wrote: > 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 <https://www.ebi.ac.uk/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 Given that this annotation source is no longer maintained, I decided to 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: > > - rat.db0 > - chicken.db0 > - zebrafish.db0 > - mouse.db0 > - bovine.db0 > - human.db0 > > 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. > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel