[Bioc-devel] RFC: Naming scheme for organism level annotation data packages

[Seth Falcon]

Wolfgang Huber <huber at ebi.ac.uk> writes:

> Dear Seth,
>
>>> One possible option I wanted to throw into the ring to solve the
>>> identifier system problem and at the same be at least conceptually
>>> prepared for annotations of multi-species systems (e.g. host-pathogen,
>>> say, man/anopheles/plasmodium) would be to use name of the name of
>>> identifier system (EG) as the prefix rather than "org".
>>
>> That was something we discussed.  The down sides of that are:
>>
>>   - What would you put for an updated version of the YEAST package?
>
>
> how about sgd.sc.db or sc.sgd.db or just sc.db?
> given that SGD is responsible for the systematic names of the genes in
> the S.cerevisiae genome:
>   http://www.yeastgenome.org/help/yeastGeneNomenclature.shtml
>
> yeast is a very simple and clean example compared to the state of
> affairs in many other species and associated scientific communities,
> so in that case stating "SGD" might be unnecessary, due to its
> undisputed central role. So it may not necessarily be the best example
> for us for deciding how to do things in general.
>
> In Sc, it is much more apparent what a "gene" is: in other organisms,
> the mapping between what are the actual proteins in the cell and the
> loci on the DNA where they are transcribed from is more complex, in S
> cerevisiae it is so simple that one often doesn't even think about it.

Those are fine suggestions.  Do you (or others) think it is worth
having a common prefix for all organism level packages?

   org.sgd.Sc.db
   org.eg.Hs.db
   org.eg.Mm.db

Since we don't (yet) have a super fancy dynamic webapp that allows
users to slice and dice their package display, there is some immediate
benefit to having similar packages sort next to each other.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org