[BioC] Annotation Questions

[John Zhang]

>
>Thanks for your response.  I have a few more questions...
>
>1. I was following along the "How to use AnnBuilder" vignette and got to the
>end.  I was not sure at the end on how to use the data package I had built.
>Where can I go to find out more information on how to use a data package and
>data packages in general? 

Using hgu95av2 as an example, hgu95av2() shows a list of the environment objects 
contained with some quality control maesurements and ?hgu95av2 gives the data 
sources used to build the data package. Each environment object contained by the 
packages has a help file that can be shown by typing ?objectName 
(?hgu95av2SYMBOL). Common opertions for a given environment object include:

ls(objectName) (ls(hgu95av2SYMBOL)) 
lookUp(keys, package, element) (lookUp(c("40576_f_at","1091_at"), "hgu95av2", 
"SYMBOL"). The developmental version of annotate is required)   

>
>2. In your vignettes on AnnBuilder I can see that you are loading up your
>base file, specifying which sites to download data, then there are calls to
>parsers.
>For the next step I would like to know the main functions responsible for
>mapping.
>I would like to know if there are some functions I can use for mapping or
>ones I can look at to model after.

fileMuncher is the one that does the mapping. But if you have your clones mapped 
to either GenBank, UniGene, LocusLink, or IMAGE ids, you can just use 
ABPkgBuilder to build the data package. 

>
>3. Can you suggest a good resource for takig XML information
>and dumping it into a database?

Depending on what application language you will be using. For R, the XML package 
is useful.

>
>thanks very much,
>Annie.
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084