[BioC] How are GO2PROBE built

[john seers (IFR)]

Hi Marc and Sean

Thank you both for your answers. 

When I said ad-hoc I did not mean to sound critical; it was just coming
at me a bit ad-hoc because I could not find an overview of it. I think
the change to AnnotationDbi happened at some point so there seemed to be
a lot of choices and without the knowledge I could not make sense of it.
Plus dealing with some unusual arrays did not help me.

However Sean's short description is great and I will have a look at
AnnotationDbi.html with interest. 

Thank you.

John Seers





 
---

-----Original Message-----
From: Marc Carlson [mailto:mcarlson at fhcrc.org] 
Sent: 02 October 2008 17:09
To: john seers (IFR)
Cc: Sean Davis; Oura Tomonori; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] How are GO2PROBE built

Hi John,

The annotation system is not meant to be ad hoc although it has been
changing a lot recently as we have migrated to a much more powerful
database centric system.  Please have a look at the vignettes on this
page to see more current information:

http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html

Please let me know if you have any further questions.


  Marc



john seers (IFR) wrote:
>  
>
> Hi Sean
>
> Turning this into a more general question. Whenever I have to deal 
> with a new type of Affymetrix array I seem to have to root around 
> Bioconductor packages to find out how it is annotated etc. By the time

> I come around to do it again it has all changed and is done in a 
> different way to how it was done before. My difficulty is it all feels

> a bit adhoc and comes at me in bits and pieces. Also I always feel 
> there is probably a better way to do it that I am missing.
>
> Is there anywhere information that gives a better big picture that 
> pulls it together a bit? What are the foundation designs/philosophy 
> that all the packages are following? Is there a routemap type document

> that describes Bioconductor's approach to all this?
>
> Any pointers to useful information gratefully received.
>
> Thanks.
>
>
> John Seers
>
>
>
>
>
>
>  
> ---
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean 
> Davis
> Sent: 02 October 2008 11:55
> To: Oura Tomonori
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] How are GO2PROBE built
>
> On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori 
> <tomonori.oura at gmail.com>
> wrote:
>   
>> Dear BioC,
>>
>> How are the mappings of Affymetrix probe ids to Gene Ontology terms 
>> in
>>     
>
>   
>> metadata package provided by Bioconductor build?
>>
>> I am trying to use some gene set analysis packages and find some 
>> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but 
>> another package use the external gene set definition, such as MSigDB.
>>
>> So I want to know the criteria for select specific GO term among 
>> possible terms for each probe id in Bioconductor.
>> I already read the documents about AnnBuilder package, however.
>>     
>
> To make a long story short, the annotations available from affy are 
> mapped to Entrez Gene IDs.  Then, the information from Entrez Gene--in

> this case, gene ontology--is mapped to affy id.  The dates associated 
> with the data, the source of the data, and how the data are mapped 
> will all affect the final mapping of affy ID to gene ontology.  The 
> nice thing about gene ontology analyses is that they are typically 
> based on "sets" of genes making it much less important to start with 
> EXACTLY the same gene ontology mappings.  In fact, in practice, it 
> will be pretty difficult to do so.
>
> If you want to see the details of the current Bioconductor annotation 
> package build process, you want to read the AnnotationDbi SQLForge 
> vignette, as AnnBuilder is outdated.
>
> Finally, if I have misunderstood your question, perhaps you could 
> clarify.
>
> Sean
>
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