[BioSQL-l] The bioentry and biosequence tables

[Peter]

On Wed, Dec 17, 2008 at 2:49 PM, Hilmar Lapp <hlapp at gmx.net> wrote:
>
> The bioentry table is for any biological database entry with a stable and
> unique identifier.
>
> In practical terms most of these will be sequence database entries, but they
> don't have to be. Among the not so far fetched examples are gene
> records/models (such as from LocusLink or Entrez Gene) and (e.g. EST or
> protein) sequence clusters.

Yes - as another example I was thinking you could import an NCBI
Protein Tables (PTT) table like this, you'd have lots of seqfeature
entries but no actual sequence.

> A (at present) more exotic example would be museum specimen records.
>
>> Does doing it as a separate table speed up accessing the core
>> (non-sequence) bioentry information?
>
> Possibly. To what extent will depend on the RDBMS, obviously. But at least
> several years ago, when BioSQL was first designed, some RDBMSs would indeed
> be faster in full table scans if the table didn't contain an LOB.

OK - I thought that might have been the case.

> The way to look at it conceptually for us has been similar to object
> orientation. The bioentry table is the base table for all biodatabase
> entries, and the biosequence table is in joined for derived objects that
> also have a sequence.
>
> Does that make sense?

Yes it does.  Thanks.

Peter