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

Marc Carlson mcarlson at fhcrc.org
Wed Nov 7 01:41:43 CET 2007

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 =
>                    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
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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

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.



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