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

Wolfgang Huber huber at ebi.ac.uk
Sat Jul 21 14:06:00 CEST 2007

Hi Seth,

sounds good to me.

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".

  Best wishes

  Falcon ha scritto:
> Hello all,
> We are working on new and improved versions of humanLLmappings (along
> with rat and mouse).  The contents will be similar, but we are making
> some significant changes.  In particular, we are trying to make the
> data maps as similar as possible to those found in the common
> Affymetrix chip-based packages.  This will make programatic use of the
> packages easier.
> For human, mouse, and rat, the central ID will be Entrez Gene.  This
> will not be the case for all organism level packages,
> e.g. S. cerevisiae where EG is not the ID chosen by the research
> community.  Therefore, we propose the following naming scheme for new
> organism level annotation data packages:
>     org.<organism>.db
> where <organism> is the UniGene organism abbreviation [1].  To start
> with, then, we will have:
>    org.Hs.db
>    org.Mm.db
>    org.Rn.db
> The 'org' prefix identifies the package as organism wide and will make
> it easy for these packages to sort next to each other.  Using UniGene
> organism abbreviations gives us a short, specific, and reliable
> abbreviation.  The 'db' suffix indicates that these packages will be
> backed by a DB (SQLite) and use the AnnotationDbi interface.
> One possible downside is that if an alternative primary ID emerges
> (e.g. an ensembl based) then we would need to add a way to
> distinguish.  But we felt it was easier to cross that bridge when we
> get there.
> Comments?  Suggestions?  Concerns?  Send them along.  If we don't hear
> anything by next Wednesday 25 July, we will move forward with this
> proposal.
> Best,
> + seth
> [1] There is probably a more graceful way, but you can find an
> abbreviation by browsing here__ and clicking on the number in the
> right column in the row for the organism of interest.


Best wishes

Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber

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