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

[Wolfgang Huber]

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.

   Best wishes
	Wolfgang
> 
>   - How would you indentify organism-level packages?  [Perhaps your
>     point is that this may not really be all that useful so isn't
>     worth considering].
> 
> + seth
>