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

[Paul Shannon]

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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>>
>>
> 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