[BioSQL-l] location type

[Thomas Down]

On Tue, Oct 15, 2002 at 09:56:24AM -0700, Hilmar Lapp wrote:
>
> > > What I suggested is not really denormalization. You're 
> > right though, 
> > > there's duplication. If the coordinate types (which I mentioned 
> > > further down in the email in the part you cut) are just moved from 
> > > being location_qualifier_value associations to FKs on 
> > location, then 
> > > there isn't really duplication anymore either. Or am I missing 
> > > something?
> > 
> > It's still duplication for the cases where the actual maxima 
> > and minima
> > are in location_qualifier_value.
> 
> What would be duplicated? Can you be specific? (I don't see it.)

Because the fact that a given location is fuzzy is recorded
both by putting the `fuzzy' term in the relevant slot onto the
location itself, and by the fact that it has one or more
location_qualifier_value entries joined to it.

> >  If
> > you want to work around it in the database, why not just put a boolean
> > `here be qualifiers'  flag on seqfeature_location?
> 
> This was more or less the suggestion my first email ended in: have a FK 
> to ontology_term that denotes an encoded type. Since whether or not 
> there be qualifiers strictly depends on the type, this is similar to 
> a flag except that it uses controlled vocabulary and is more explicit. 
> Is this too explicit to you, or too much information encoded?

To be honest, I'm not too bothered about the exact mechanism.  My
point of view is that while the actual details about precisely HOW a given
span is fuzzy are still encoded by entries in location_qualifier_value,
anthing that goes in seqfeature_location is redundant from a
strict normalization point of view.  However, I can see now why
it's a necessary optimization from the point of view of your adaptors -- 
go for it.


      Thomas.