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

Seth Falcon sfalcon at fhcrc.org
Mon Jul 23 15:58:07 CEST 2007

Vincent Carey 525-2265 <stvjc at channing.harvard.edu> writes:
> wouldn't the sorting be more informative if we had, for example
> org.Hs.eg.db -- entrez gene
> org.Hs.en.db  -- ensembl, maybe


> i.e., provider would nest within organism.  if it is not intended
> to have multiple providers, take it out
> org.Hs.db
> org.Sc.db
> i would expect to scan for organism first, then for provider within
> organism if we are going to distinguish these.
> if the justification for the "eg" is clear in earlier posts, disregard
> this ... i did not read them closely enough to remember now.

Well, we don't have multiple providers at this time [*] and it isn't clear
whether, for exampple, en based data could simply be integrated into
the same DB.  So it is simply not clear whether including the provider
in the name is a good idea.

[*] We do have different providers for different organisms.

So I think the revised choice is between your two suggestions:

   org.Hs.eg.db   and in general org.<org>.<provider>.db



+ seth

Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

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