You need to scroll down that script a ways... Look for 'yeast'. On Mon, Oct 5, 2015 at 6:11 AM, James W. MacDonald <jmac...@uw.edu> wrote:
> Hi Marc, > > That script has this in it: > > ## For now just get data for the ones that we have traditionally supported > ## I don't even know if the other species are available... > speciesList = c("chipsrc_human.sqlite", > "chipsrc_rat.sqlite", > "chipsrc_chicken.sqlite", > "chipsrc_zebrafish.sqlite", > # "chipsrc_worm.sqlite", > # "chipsrc_fly.sqlite", > "chipsrc_mouse.sqlite", > "chipsrc_bovine.sqlite" > # "chipsrc_arabidopsis.sqlite" ## this is available and could be > "activated" > ## But to activate arabidopsis, remember you have to pre-add the > tables... > # "chipsrc_canine.sqlite", > # "chipsrc_rhesus.sqlite", > # "chipsrc_chimp.sqlite", > # "chipsrc_anopheles.sqlite" > ) > > And there is no mention of yeast anywhere. If I search all the scripts for > say 'INSERT INTO pfam', I get > > custom_anno/script/bindb.sql > 328:INSERT INTO pfam > > pfam/script/srcdb_pfam.sql > 202:-- INSERT INTO pfamb > > organism_annotation/script/bindb_yeast.sql > 441:-- INSERT INTO pfam > > yeast/script/bindb.sql > 241:-- INSERT INTO pfam > > The first one is just doing all the metadata tables, and the other three > are in code blocks that are commented out. Is it possible that you used a > script that didn't make it into svn? > > Jim > > > > On Sun, Oct 4, 2015 at 2:36 PM, Marc Carlson <mrj...@gmail.com> wrote: > >> 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 >>> >> >> > > > -- > 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