[BioC] advantages of annotation packages

[Martin Morgan]

On 05/10/2013 01:17 AM, Rameswara Sashi Kiran Challa wrote:
> Hi All,
>
> Could anyone please elucidate advantages of having an Annotation package
> for an organism or point me to any documentation that clearly lists all the
> various thoughts behind coming up with an Annotation package.
>
> Will not having a data frame in R (with rows as genes and columns as
> various types of annotations like GO, KEGG, Unigene, etc) suffice? What are

One aspect not mentioned is that one gets to exploit R's packaging system to 
provide easily distributed and documented versions of the data. Suppose you 
created the package eight months ago and have forgotten some of the detaiils. 
Easy, check out the package description and help page. Say you're working with a 
couple of colleagues, and you've been relatively disciplined about incrementing 
the annotation package when your data changes (or are using a public Bioc 
annotation package, with versions strictly tied to R / Bioc releases). Easily 
spot when unusual results are due to differences in data version (hence the 
frequent request for the output of 'sessionInfo()' on this mailing list) and 
adopt / instill 'best practices' that make sure everyone on the team (including 
yourself, even if your team is only 1) are using the same version.

Martin

> the advantages of having a AnnodbBimap objects and building a package? Are
> there any technical benefits like faster access of information?
>
> Thanks for your time,
>
> -Sashi
>
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