[BioC] agilent zebrafish array annotation

[Georg Otto]

Marc Carlson <mcarlson at fhcrc.org>
writes:

> Georg Otto wrote:
>> Hi,
>>
>> I started to use the agilent zebrafish array and I am using
>> bioconductor packages (limma and others) for the data analysis as I
>> did already with the Affymetrix zebrafish array. I noticed that unlike
>> for the Affymetrix zebrafish array, there is no annotation package for
>> the Agilent zebrafish array, but there are packages for the Agilent
>> human, mouse and rat arrays.
>>
>> Since I have some experience in creating custom annotation
>> environments (e.g. using biomart) I would be willing to volunteer in
>> generating an annotation package for the Agilent zebrafish
>> array. However, it is not quite clear to me, how for example the
>> mgug4104a.gb or other packages of this kind were generated. Reading
>> the vignettes of the AnnBuilder and AnnotationDbi packages did not
>> help me very much either.
>>
>> Therefor my question is: Is the package creation process documented
>> somewhere? Is the code for the package generation available somewhere?
>> As I said, I would be willing to generate the annotation package and
>> contribute this to the community, but I do not know where to start.
>>
>> Best,
>>
>> Georg


>
> HiGeorg,
>
> Right now there are two styles of annotation package.  The newer format 
> is generated from code in the very latest bleeding edged version of 
> AnnotationDbi (from the devel branch), and the older format is generated 
> from AnnBuilder.  It is preferable to use the newer code in 
> AnnotationDbi, but this requires that your organism be supported first.  
> As of right now, zebrafish is not a supported organism for the newer 
> packages, but this is not set in stone.  If you would be willing to work 
> with me a little bit and be slightly more patient, we can try to rectify 
> this situation together, but otherwise you are going to have to use the 
> older AnnBuilder package to make your zebrafish packages. 
>
> Making a vignette for AnnBuilder is mostly about calling the 
> ABPkgBuilder() function with the correct parameters and using properly 
> formatted inputs.  Once zebrafish is a supported organism, the process 
> for making a new package using AnnotationDbi's SQLForge functions would 
> be very similar.  I will be happy to help you with either of these 
> processes.
>
>
>     Marc

Hi Marc,

thanks a lot for your quick answer and your offer to help!

Of course I would be highly interested  to have zebrafish in the list
of supported organisms and I am willing to contribute to that. So I
would like to hear what should be done and how I should start. From
reading briefly through the AnnotationDbi documentation my
understanding is, that a supported organism has a support database as a
basis for the creation of annotation packages. Would it be a good idea
to start creating such a support database for zebrafish, including
data from NCBI, but maybe also Ensembl and ZFIN (the zebrafish
database)?

In the meantime (since I need to annotate the microarray result I have
soon), I will start to create a simple old-style package using
AnnBuilder.

Georg