Re: [Obo-discuss] taxonomy folder in CVS

[Michael A. (Genetics) <ma...@ge...>]

Two points on this.

1. The general point. I really do not think that this group should get
into the taxonomy question.  There is a _huge_ debate in the community
about the pros and cons of Linnean vs phylocode etc. There is also,
as Judy says, a huge amount of work going on with the ToL, Species2000,
GBIF etc.

2. The taxonomy maintained at the NCBI and shared by the EBI and DDBJ makes
NO claims to represent phylogeny.  It is very much a pragmatic tool. It
_does_ use many taxonomic and systematic experts to maintain its various
sections, for example the Diptera (flies) are maintained by the foremost
Dipteran systematicist. It does use the Linnean system, but that is
because that is by far the most widely accepted system. Its purpose
is ONLY to act as a structured controlled vocabulary - so that consistent
species etc names are used in the nucleic acid and protein databases.

3. Pankash raises two reasons why it is inadequate for Gramene:

i) NCBI's taxonomy is  'incorrect': then the grass community should work
with the NCBI to help them get it 'right'.
ii) NCBI's taxonomy is incomplete. This _is_ a problem because to get into
the NCBI database the species/strain/isolate etc MUST have an associated 
species.

ii) is more of a problem, ideally it would be good if the NCBI could
expand their coverage.

We could put this on OBO, but surely its real utility is _within_ Gramene ?

Michael