[Open-bio-l] BioSQL schema: some questions

[Hilmar Lapp]

> -----Original Message-----
> From: Ewan Birney [mailto:birney@ebi.ac.uk]
> Sent: Saturday, April 27, 2002 4:08 AM
> To: Chris Mungall
> Cc: Hilmar Lapp; OBDA BioSQL (E-mail); 
> gmod-devel@lists.sourceforge.net
> Subject: Re: [Open-bio-l] BioSQL schema: some questions
> 
> 
> On Fri, 26 Apr 2002, Chris Mungall wrote:
> 
[...]
> > 
> > > 9) Why is there molecule in Biosequence (and not in 
> Bioentry)? I.e.,
> > > would there be Biosequence entries of different molecule 
> (mRNA, DNA,
> > > ...) for a particular Bioentry? If so, this is contradicted by the
> > > identifying relationship to Bioentry (there is a UK on the FK).
> > 
> > pass; there was a thread on bioperl a while ago about 
> molecule type vs
> > alphabet
> > 
> 
> molecule = where it came from (eg mRNA)
> 
> alphabet = how it is encoded (DNA/RNA etc)
>

Shouldn't then molecule be an attribute of Bioentry? Likewise, shouldn't alphabet be added to Bioentry?
 
> 
> > > 17) Aren't Dbxref.dbname and Biodatabase.name redundant? 
> Shouldn't there
> > > be a FK?
> > 
> > pass
> > 
> 
> Not dbref.dbnames will be biodatabase.name, in particular in 
> things like
> swissport which going link-tastic v. quickly.
> 

Sorry. I'm not sure I understand what you mean.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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