[Open-bio-l] Fwd: [BioSQL-l] Taxa

[Hilmar Lapp]

Hmm. I could take zero response as consent to all changes 
proposed -- would be great actually. To make double sure those who 
might have wanted to see this proposal did see it I'm resending and 
cross-posting it ... Shout now if you're concerned or don't complain 
later.

Also, if this is the first time you see this and it is important to 
you, you're probably not on the biosql mailing list although you 
should be. Please subscribe (see footer for list info) since this is 
the last time I'm going to cross-post.

	-hilmar

Begin forwarded message:

> From: "Hilmar Lapp" <hlapp@gnf.org>
> Date: Wed Aug 28, 2002  02:23:41  PM US/Pacific
> To: "Biosql" <biosql-l@open-bio.org>
> Subject: [BioSQL-l] Taxa
>
> I propose to make the following changes to tables Taxa and
> Bioentry_Taxa, ranked by decreasing priority (still, I'd like to
> make all of these changes).
>
> 1) Introduce UK constraints. This makes it much safer (and
> potentially faster due to amenability to caching) to find records).
> My suggestions for UK candidates are common_name, full_binomial (see
> 2.), and ncbi_taxa_id. (There are no UKs yet.)
>
> 2) Introduce an additional column full_binomial ('full' in the
> bioperl Bio::Species sense: with ssp if applicable). I think this is
> going to be searched against quite frequently, and I just don't
> think it's very practical to always extract this out of full_lineage.
>
> 3) Collapse Taxa and Bioentry_Taxa into one and add Taxa_Id as a
> nullable FK to Bioentry. Having this additional association table
> doesn't add any functionality we'd like to use, but instead can only
> decrease performance and enforceability. Also, it necessitates
> otherwise pointless code in the adaptors.
>
> 4) For consistency, rename Taxa and all Taxa related columns to
> Taxon (Taxa is plural, all other table names are singular).
>
> What do people think? Any outcries? If I make these changes,
> adaptors in different projects will have to be changed (I'll change
> the ones involved in Bioperl-db).
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>
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--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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