[BioC] Problem with GOPkgBuilder from AnnBuilder when trying to create an updated GO data package

Thu Sep 27 23:30:05 CEST 2007

Dear Stefan,

> Thanks for your mail.
> I feel there is some misunderstanding here. I am not after a monthly
> update of Bioconductor annotation packages at all. I just would like to
> use the GO package, because I want to use the gene ontology vocabulary
> in R for my research. I would like to be able to have this up to date.
> My question is then if I want to do this, then is the GOPkgBuilder
> function of the AnnBuilder package the function to use, since this is
> what it seems from the documentation.

Yes, that is correct, but the point is that all the annotation packages 
refer to each other (and in particular each one uses the GO terms from 
the GO package), and changing such a basic package GO, without the 
others can create lots of missing links / invalid references. If you 
want to deal with that, then fine, but it is up to you.

What is your use case for upating the GO package so frequently? You will 
also need to simultaneously update your other data structures that link 
your objects of interest (e.g. reporters on a microarray) to GO terms.

An alternative is to use the biomaRt package, but again, but I'd expeczt 
that you will need to do work to postprocess the annotations and align 
them between different databases sources.

  Best wishes
   Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

>> -----Original Message-----
>> From: Robert Gentleman [mailto:rgentlem at fhcrc.org] 
>> Sent: Thursday, September 27, 2007 4:30 PM
>> To: goetz_stefan at gmx.de
>> Cc: mcarlson at fhcrc.org; bioconductor at stat.math.ethz.ch
>> Subject: Re: [BioC] Problem with GOPkgBuilder from AnnBuilder 
>> when trying to create an updated GO data package
>>
>>
>> Hi Stefan,
>>
>> Stefan Goetz wrote:
>>> Dear Marc, 
>>> thanks for your reply. Updating my R to beta version 2.6, I 
>> managed to
>>> download the GO_1.99.1 package of the last Bioconductor 2.1 release
>>> with:
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite("GO")
>>> Now I have the GO data package built from Wed Aug 29 09:16:39 2007.
>>> Great!
>>> Just for the future, dose anybody know how to make monthly 
>> GO updates of
>>> this package? Would be to use the GOPkgBuilder function of 
>> AnnBuilder
>>> package the correct way or this a more complex thing?
>>> Best regards.
>>    There is no intention, and really no way to make monthly 
>> updates of 
>> this package.  There are about 200 other packages, many built 
>> by other 
>> people that rely on the contents of this package. Getting them to 
>> coordinate their efforts every six months, is about all that is 
>> realistically possible.
>>
>>    Monthly updates of GO you are pretty much going to have to 
>> do on your 
>> own, and what every you do, do not build a package and give 
>> it the same 
>> name as this package.  You could try relying on biomaRt for a more 
>> interactive approach.
>>
>>
>>     best wishes
>>       Robert
>>
>>> Stefan
>>>
>>>
>>>> -----Original Message-----
>>>> From: mcarlson at fhcrc.org [mailto:mcarlson at fhcrc.org] 
>>>> Sent: Thursday, September 27, 2007 2:45 AM
>>>> To: Stefan Goetz
>>>> Cc: bioconductor at stat.math.ethz.ch
>>>> Subject: RE: [BioC] Problem with GOPkgBuilder from AnnBuilder 
>>>> when trying to create an updated GO data package
>>>>
>>>>
>>>> Quoting Stefan Goetz <goetz_stefan at gmx.de>:
>>>>
>>>>> Well, I'm new to BioConductor and R and maybe missing some 
>>>> details but: 
>>>>>> GO() 
>>>>> returns: 
>>>>> Quality control information for  GO 
>>>>> Date built: Created: Tue Sep  5 18:55:54 2006  
>>>>> etc.
>>>>>
>>>>> and
>>>>> ?GO return:
>>>>>
>>>>> GO(GO): Bioconductor annotation data package:
>>>>> Description:
>>>>> The annotation package was built using a downloadable R package -
>>>>> AnnBuilder (download and build your own) etc...
>>>>>
>>>>> So my question still is how to use GOPkgBuilder from 
>> AnnBuilder when
>>>>> trying to create an updated GO data package 
>>>>> (the one by default on the BioConductor site is from: Tue Sep  5
>>>>> 18:55:54 2006 and the Gene Ontology is evolving fast)
>>>>> Any ideas/help somebody?
>>>>> Many thanks, 
>>>>> Stefan
>>>>>
>>>>> PD.: AnnBuilder is from Bioconductor, you are from CRAN? Is there
>>>>> something on CRAN for GO I missed and if so how is this 
>>>> package called?
>>>>> Thanks!)
>>>> It really sounds like maybe you should download the very 
>>>> latest version of the
>>>> GO package from our development repository which was made 
>>>> only weeks ago.  We
>>>> acknowledge that GO is a fast moving target and that is why 
>>>> we build entirely
>>>> new versions of GO every 6 months.  The very latest version 
>>>> can always be found
>>>> right here:
>>>>
>>> http://www.bioconductor.org/packages/2.1/data/annotation/
>>>
>>> I hope this helps,
>>>
>>>     Marc
>>>
>>> _______________________________________________
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>> http://news.gmane.org/gmane.science.biology.in> formatics.conductor
>> -- 
>> Robert Gentleman, PhD
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M2-B876
>> PO Box 19024
>> Seattle, Washington 98109-1024
>> 206-667-7700
>> rgentlem at fhcrc.org
>>
> 
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