[Bioc-devel] Extending annotation packages

Sean Davis 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
>> flag.
> 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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