Hi Paul, Marc, <hype> We at the Sanger Institute, having sequenced most of this beast's genome (http://www.sanger.ac.uk/Projects/P_falciparum/), have developed arrays for P. falciparum (the Affymetrix PFSANGER array), as well as for rodent malarias P. berghei and P. chabaudi (Affy, RMSANGER). </hype> As a result we are frequently generating/updating annotation datasets for these organisms. I should point out that the data in NCBI/EMBL have not been updated recently, and there have been many gene model/annotation etc changes since sequence submission. The most current dataset are in GeneDB (http://www.genedb.org/genedb/malaria/). That said, ~10 days ago we had a week-long annotation workshop/jamboree that has refined many gene models and updated many product calls, GO terms etc etc. We are currently collating and QCing the annotation changes, with a view to updating GeneDB in the near future, plus other public data repositories. Thus, using the "standard" annotation package pipeline might perhaps not be appropriate, at least not in the interim? Cheers, al > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of > Paul Shannon > Sent: 05 November 2007 22:59 > To: Marc Carlson > Cc: bioc > Subject: Re: [BioC] how to build a GOstats-compatible > annotation package forplasmodium falciparum? > > > Hi Marc, > > You ask: > > > Is it in fact a high priority for the > > community to collate a set of annotation packages about > p.falciparum? > > > > > I don't have any data on, or any real feeling for, how much use an > annotation > package for falciparum would see in the bioc community. A few > points in its favor are > > 1) falciparum is not an orphan organism: the gene ontology > project supports > it (along with many other organisms, of course) > > 2) funding for malaria research is probably at an all-time high > > 3) We (and many others) are actively searching for, and testing, > malaria vaccine candidates. > Any progress made in this will result in lives saved. > Judicious use of > GOstats can be very helpful in, say, identifying liver-stage > specific > antigens, or gaining insight into the mechanisms of > cytoadhesion in > pregnancy malaria. > > I don't know if many would find this compelling, but for me, the > uncertainty > of heavy use -- would an annotation package be used my many? > -- might be offset by the real-world benefits that would > likely accrue from > even limited use > of the package. > > But of course I don't know how many high priority items you are > already trying to juggle. > It could be many, and their real-world benefits may be just as > compelling as falciparum > annotation: progress on other diseases, attaining new & fundamental > understanding of > biological processes, developing new analytical techniques. > > Is it possible to reduce the task from 'create a general > purpose bioc > annotation package' to > simply 'assemble the few environments needed by GOstats'? > If that's > possible, and if you > could give me a few tips, perhaps I could undertake this myself. > > Cheers, > > - Paul > > > > > On Nov 5, 2007, at 2:07 PM, Marc Carlson wrote: > > > Paul Shannon wrote: > >> I'm familiar with the YEAST data package, and the many > chip-specific > >> annotation packages -- all of which work very nicely with GOstats. > >> > >> GO offers annotation for p.falciparum, the malaria parasite. What > >> would it take to put that into an R data package which > will work with > >> GOstats? > >> > >> Thanks! > >> > >> - Paul > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/ > >> gmane.science.biology.informatics.conductor > >> > >> > > This is a good question. The short answer is that it is entirely > > possible to do it, but that it's not supported by the new > annotation > > pipeline at the moment. > > > > The long answer is that I would be delighted to add this > organism if > > there is a strong desire for it by the community. We are always > > looking > > for feedback to help us know which things we should be > supporting, and > > this includes indications about which organisms are being studied > > enough > > to merit an annotation package. For me it's not a question > of whether > > or not I will add new stuff to the annotation packages. > It's really a > > question of which stuff I should be working on first. > > > > But because we want the annotation packages to be maximally > helpful to > > the largest possible group of people, we are always need > information > > about what you guys need. > > > > > > So my question for you is this: Is it in fact a high > priority for the > > community to collate a set of annotation packages about > p.falciparum? > > > > > > Marc > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/biocondu> ctor > Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Hi Paul, if you want to perform an enrichment analysis for the GO terms you can also look at the topGO package. It works also in the cases in which there is no chip-specific annotation package. What you need is a mapping between genes and GO terms. This mapping can be provided either as "gene to GO trems" or as "GO term to genes" and they should be lists indexed either by the genes or by GO terms. You can take a look at the man page of "annFUN.GO2genes" function. I hope this helps, Adrian On 11/5/07, Paul Shannon <pshannon at="" systemsbiology.org=""> wrote: > Hi Marc, > > You ask: > > > Is it in fact a high priority for the > > community to collate a set of annotation packages about p.falciparum? > > > > > I don't have any data on, or any real feeling for, how much use an > annotation > package for falciparum would see in the bioc community. A few > points in its favor are > > 1) falciparum is not an orphan organism: the gene ontology > project supports > it (along with many other organisms, of course) > > 2) funding for malaria research is probably at an all-time high > > 3) We (and many others) are actively searching for, and testing, > malaria vaccine candidates. > Any progress made in this will result in lives saved. > Judicious use of > GOstats can be very helpful in, say, identifying liver-stage > specific > antigens, or gaining insight into the mechanisms of > cytoadhesion in > pregnancy malaria. > > I don't know if many would find this compelling, but for me, the > uncertainty > of heavy use -- would an annotation package be used my many? -- might > be offset by the real-world benefits that would likely accrue from > even limited use > of the package. > > But of course I don't know how many high priority items you are > already trying to juggle. > It could be many, and their real-world benefits may be just as > compelling as falciparum > annotation: progress on other diseases, attaining new & fundamental > understanding of > biological processes, developing new analytical techniques. > > Is it possible to reduce the task from 'create a general purpose bioc > annotation package' to > simply 'assemble the few environments needed by GOstats'? If that's > possible, and if you > could give me a few tips, perhaps I could undertake this myself. > > Cheers, > > - Paul > > > > > On Nov 5, 2007, at 2:07 PM, Marc Carlson wrote: > > > Paul Shannon wrote: > >> I'm familiar with the YEAST data package, and the many chip- specific > >> annotation packages -- > >> all of which work very nicely with GOstats. > >> > >> GO offers annotation for p.falciparum, the malaria parasite. What > >> would it take to > >> put that into an R data package which will work with GOstats? > >> > >> Thanks! > >> > >> - Paul > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor at stat.math.ethz.ch > >> https://stat.ethz.ch/mailman/listinfo/bioconductor > >> Search the archives: http://news.gmane.org/ > >> gmane.science.biology.informatics.conductor > >> > >> > > This is a good question. The short answer is that it is entirely > > possible to do it, but that it's not supported by the new annotation > > pipeline at the moment. > > > > The long answer is that I would be delighted to add this organism if > > there is a strong desire for it by the community. We are always > > looking > > for feedback to help us know which things we should be supporting, and > > this includes indications about which organisms are being studied > > enough > > to merit an annotation package. For me it's not a question of whether > > or not I will add new stuff to the annotation packages. It's really a > > question of which stuff I should be working on first. > > > > But because we want the annotation packages to be maximally helpful to > > the largest possible group of people, we are always need information > > about what you guys need. > > > > > > So my question for you is this: Is it in fact a high priority for the > > community to collate a set of annotation packages about p.falciparum? > > > > > > Marc > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

Paul Shannon wrote: > Hi Marc, > > If (as seems quite possible) no one has time right now to do a proper > malaria annotation package, > can you tell me how I can get started with creating the minimal data > needed for > GOstats? > > I hope that if I were to emulate the YEASTGO environment from the > YEAST package -- creating > a PFALCIPARUMGO environment, for instance -- that that might be all > that GOstats needs. > > Would that indeed work? If so, and assuming I could build a properly > structured environment, > a puzzle remains: one constructs a GOHyperGParams object specifying > > annotation = 'YEAST' > > What would the equivalent argument be for a home-brewed (and minimal) > annoation > object? I imagine that hyperGTest does some magic to map from "YEAST" > to the > YEASTGO environment. > > > params = new ("GOHyperGParams", geneIds = unique (deleted), > universeGeneIds = universe, > annotation = "YEAST", > ontology = "BP", pvalueCutoff = 0.01, conditional = > TRUE, > testDirection = "over") > > > Got any sugeestions? Cautions? > > Thanks! > > - Paul > > On Nov 5, 2007, at 2:07 PM, Marc Carlson wrote: > >> Paul Shannon wrote: >>> I'm familiar with the YEAST data package, and the many chip- specific >>> annotation packages -- >>> all of which work very nicely with GOstats. >>> >>> GO offers annotation for p.falciparum, the malaria parasite. What >>> would it take to >>> put that into an R data package which will work with GOstats? >>> >>> Thanks! >>> >>> - Paul >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> This is a good question. The short answer is that it is entirely >> possible to do it, but that it's not supported by the new annotation >> pipeline at the moment. >> >> The long answer is that I would be delighted to add this organism if >> there is a strong desire for it by the community. We are always looking >> for feedback to help us know which things we should be supporting, and >> this includes indications about which organisms are being studied enough >> to merit an annotation package. For me it's not a question of whether >> or not I will add new stuff to the annotation packages. It's really a >> question of which stuff I should be working on first. >> >> But because we want the annotation packages to be maximally helpful to >> the largest possible group of people, we are always need information >> about what you guys need. >> >> >> So my question for you is this: Is it in fact a high priority for the >> community to collate a set of annotation packages about p.falciparum? >> >> >> Marc Well I plan to do this. But it's just not going to happen overnight. I am booked right now with a homology implementation and I also have to finish getting part of the promised pipeline in place for our other annotation package collaborators so that they can update their packages to the newer format for the upcoming release. This means that I may not get to start this for a couple of months, but it has been added to my todo list. For now, I recommend that you try to use the AnnBuilder package. We are planning to retire this package along with the style of annotation package that it spawns so this is definitely NOT a good long term solution and is to be used for the short term ONLY. But I think that it will probably get you the quick fix that you need. http://bioconductor.org/packages/2.1/bioc/html/AnnBuilder.html Marc