Hi Asis,

So to get the most thorough answers to questions about bioconductor, 
please post them here at the official bioconductor list.  The core team 
is a small group and we can't possibly presume to know as much as the 
3000 other bright and talented people who subscribe to our list.  ;)

Answers to your questions:
1) GOALLFrame has many annotations because it is an expansion of GOFrame 
based on the Gene Ontology.  The ontology is a DAG, and so it's graph 
like structure means that there are many ancestor terms for any given 
term which are (implicitly) related whenever a specific term is chosen.  
The GOALLFrame adds back those terms.
2) The extra GO terms come only from GO.db.  The gene ids are simply 
repeated as appropriate when ancestor GO terms are added.
3) The current query used to extract parent terms does not discriminate 
based on the type of relationship.  It just gets all the GO terms that 
are ancestors to the current set of terms and adds them to the list as 
also mapping to the same gene ids.  The other code that was intended to 
be used downstream of this step should be doing something reasonable for 
you (with respect to relationship type) already.  And since this is 
basically intended to be an annotation resource, it does not really make 
sense to filter results at this stage in the game.  The GOAllFrame is 
meant to basically replace what you would find in a GO2ALL mapping from 
an annotation package.  So it's not intended to be filtered in any way.

I hope this explains things for you.  Please let me know if you have 
other questions,


   Marc



On 10/02/2013 09:26 AM, Maintainer wrote:
> Dear Bioconductor Maintainers,
>
> thank you for providing such a useful tool-set.
>
> I have a question regarding the package AnnotationDbi, specifically 
> the classes GOFrame and GOALLFrame.
>
> During a GO Enrichment Analysis I create a data frame with Arabidopsis 
> thaliana GO annotations and from that first a GOFrame and than from 
> this GOFrame a GOALLFrame. Checking the result with
>
> nrow(  getGOFrameData(  athal.go.all.frame ) ) # The GOAllFrame
>
> and comparing it with
>
> nrow( athal.go.frame )                                         # The 
> GoFrame
>
> I realize that the GOALLFrame has more than 5 times more rows than my 
> original GO annotation table. If I provide
> organism='Arabidopsis thaliana'
> to the constructor of GOFrame this ratio increases even further.
>
> Unfortunately I could not find any documentation on this, so I feel 
> forced to bother you with my questions:
>
> 1) Why does GOALLFrame so many more annotations?
> 2) Why and from where does it retrieve the organism specific ones that 
> are added when a model organism like 'Arabidopsis thaliana' is provided?
> 3) I suspected that all ancestors of annotated terms are added, but 
> when I did so myself, I still got less GO term annotations? So do you 
> add ancestors of the "is_a" type and possibly other relationship types 
> like "part_of" etc. ?
>
> Please let me know your answers soon.
>
> Kind regards!
> Asis Hallab
>
>
> ---
> Asis Hallab
> Department Tsiantis
> Max Planck Institute for Plant Breeding Research
> Carl-von-Linné-Weg 10
> 50829 Köln (Cologne)
> Germany
> Phone: +49-221-5062-157
>
>
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