[BioSQL-l] Oracle support...

[Hilmar Lapp]

On Thursday, July 31, 2003, at 09:48  PM, Len Trigg wrote:

> Hilmar Lapp wrote:
>> Is your Biojava/Oracle support for biosql able to handle names
>> different from the otherwise expected Pg schema?
>
> I just thought of another question. Does the BioPerl/Oracle support
> for BioSQL handle table and field names that are the *same* as the pg
> schema (i.e. can BioPerl be used to access the mysql-port schema that
> I made, or does it assume the details of the Symgene schema). I don't
> really use perl myself, but it is conceivable that someone in our
> project might want to later on.
>

It expects the synonym-based API.

I'd be willing to make a speed comparison with the view-based API and 
switch it over speed is comparable.

Theoretically, full selects should be equal in speed. I'm not sure to 
what extent there is a difference for joins and index-key selects, and 
in 9i there may be no difference anymore, but I'd rather see it 
(unit-)tested before I believe it.

The difference at least up to 8i was that selects from a view will 
always read the row from the table (and then return only those columns 
that you requested), whereas in a select from a table if the select 
list can be satisfied from the indexes that were used it wouldn't even 
read from the table. E.g. if you selected only the primary key from a 
table, Oracle would only open the primary key index, but not the table.

Bioperl-db doesn't do partial row selects. There are some limited joins 
though (which is the same situation: those tables that don't appear in 
the select list can usually be satisfied from the index alone).

As I said, the difference if any may be minuscule. I'd just rather know 
before switching.

And at any rate I guess it's clear that that wouldn't happen now.

	-hilmar


> Cheers,
> Len.
>
-- 
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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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