Re: [GMOD-devel] NCBI Taxonomy in chado

[Scott C. <ca...@cs...>]

Hi Allen,

My only concern is that your changes be compatible with what would be
required for chado to be used by evolutionary biologists as well.
Unfortunately, I can't think of the name of their standard off the top
of my head: perhaps someone at NESCent is reading this list and can
refresh my memory?

Scott


On Tue, 2006-04-04 at 00:31 -0700, Allen Day wrote:
> Hi,
> 
> I don't know if this has been done recently, and I can't update from the
> SF repository, which is down, but I have imported the NCBI Taxonomy
> database into chado.  This required:
> 
>   * minor mangling of names.  The Taxonomy database does not have a unique
>     constraint on genus+species.  In fact, it doesn't even separate genus
>     from species, and just gives a long string that sometimes contains
>     subspecies or other junk.  I did my best to parse this.
> 
>   * schema addition of an organism_relationship table.  This is just like
>     any of the other *_relationship tables, relating two organisms with a
>     cvterm.
> 
>   * schema addition of an organismpath table.  necessary for functions
>     described below.
> 
>   * bulk load script, based on bulk GFF3 loader.  loads to organism,
>     dbxref, organism_dbxref, and organism_relationship.
> 
>   * schema addition of PL functions to populate organismpath:
>     . _fill_organismpath4node(INT,INT,INT,INT)
>     . _fill_organismpath4root(INT)
>     . fill_organismpath()
> 
>   * schema addition of PL functions to recursively query taxa:
>     . get_organism_below(INT)  [possibly rename to get_taxa_below ???]
>     . get_organism_above(INT)  [ditto]
> 
> These schema changes are entirely backward compatible.  The load script
> does not introduce lib dependencies -- just a dependency on having the
> NCBI Taxonomy database dump as local files.
> 
> Unless there are objections, I would like to check this in when SF CVS is
> functional again.
> 
> -Allen
> 
> 
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory