[Bioc-devel] Extending annotation packages

Seth Falcon sfalcon at fhcrc.org
Wed Jul 18 17:18:13 CEST 2007

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).

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.

3. Don't forget to add documentation for the objects you add to the
   package :-)

+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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