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

[Adrian Alexa]

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
> >>
> >> _______________________________________________
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> >> 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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