[BioC] Creating an OrganismDbi package with a few transcript annotations

[Martin Morgan]

On 05/16/2013 01:50 PM, Michael Lawrence wrote:
> Hi,
>
> I'd like to create an OrganismDbi package so that I can put extra
> annotations on the transcripts/genes in a TxDb package. My understanding is
> that I need a separate database package that I can join with the TxDb
> package. Do I need to make an OrgDb package? I looked into this a bit and
> it seems that there is little support for making a non-NCBI-based org
> package. Maybe I could create a new type of package with a simple table
> with a row for each transcript, including the gene symbol and whether the
> transcript is "canonical" according to UCSC. It looks like this process is
> documented here:
> http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/NewSchema.pdf.
> It also seems really involved. What's the path of least resistance here?

Hi Michael -- Marc is away for a few days. I *think* the idea is that the 
details in NewSchema are no longer required, rather, implement your extra data 
in any fashion to provide a 'select' interface, i.e.,

   keytypes
   keys
   cols
   select

following the implied API of ?keytypes. Then create an OrgDb package with

   AnnotationDbi::makeOrganismPackage

Sorry not to be more definitive in my help.

Martin

>
> Thanks,
> Michael
>
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>
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