[BioC] how to build a GOstats-compatible annotation package forplasmodium falciparum?

[Al Ivens]

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
> >>
> >> _______________________________________________
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> >> 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
> 
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