[Bioc-devel] Extending annotation packages
sdavis2 at mail.nih.gov
Wed Jul 18 21:27:46 CEST 2007
Seth Falcon wrote:
> Hi Sean,
> Sean Davis <sdavis2 at mail.nih.gov> writes:
>> I have built an annotation package, but I would like to add a couple of
>> more annotation sources (which I will build by hand). Is there an
>> accepted way of doing this if the ultimate goal is distribution? In
>> particular, I would like to add a mapping to higher-resolution
>> chromosome location information and another mapping to a boolean
> I don't think we have a recommended procedure. A few ideas:
> 1. You can contribute the annotation data package to BioC and
> distribute it there if you like. In this case, you will be
> expected to update the release version prior to each BioC release
> and to build the package against the same annotation source data
> download that we use for the other packages -- this way things like
> GO will be in sync across packages. Marc Carlson is the contact
> person for this (he is a new member of our group in Seattle;
> Nianhua is no longer in the group, but still involved in BioC on a
> volunteer basis).
That would be the plan, yes.
> 2. Is the higher-resolution chromosome location information something
> that could be applied to many existing annotation data packages or
> just yours? We hope to have some discussion at the Developer Day
> at BioC2007 about future directions for the annotation data
> packages with a focus on what newly available data should be
> included in future releases of the packages.
In addition to locations of genes on the chromosomes, I would like to
include information about the probe locations themselves, since for the
platform that I am using, these data are critical.
> 3. Don't forget to add documentation for the objects you add to the
> package :-)
But, of course. ; )
As usual, thanks, Seth.
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