[BioSQL-l] case sensitivity in biosql accessions under BioJavax/Hibernate

[James Procter]

Thanks for the reply - Mark.

Mark Schreiber wrote:
> Are there any situations where Accessions would not be case
> insensitive? 
AFAIK the public sequence, structure and gene id databases all have case
insensitive Accessions, so I'd reckon 'No' being the answer there.
However, its easy to imagine that some legacy in-house databases relying
on case sensitivity in some way.
I feel they should be case-insensitive but partly this is
> going to depend on Hibernates default behaivor and the default of the
> underlying DB. Some DB's are case insensitive by default if this is
> the case then hibernates behaivour will probably not impact this.
Again, agreed.

Assuming for the moment that accessions are case insensitive in BioSQL,
then case sensitivity should also be built into the BioSQL schema
implementations for each DB, and a case insensitive column should be
used if the DB supports it. However, regardless of whether the DB
supports that kind of attribution, the language bindings should also
have the case-insensitivity built in. In the case of Hibernate, the
bindings have to be matched to the underlying database anyway, so I
guess the problem I encountered is really due to a bug in the biojavax
schema.

of course - if case insensitivity isn't in the BioSQL spec - then its
all immaterial, so the question still remains.  Can anyone enlighten us
further ?

Jim

ps. I've started another thread for the reply regarding biosql/Bio*
object mappings.