[Biopython-dev] SwissProt DE lines and bioentry.description field in BioSQL

Hilmar Lapp hlapp at gmx.net
Sat May 16 23:42:17 UTC 2009

On May 16, 2009, at 7:14 PM, Peter wrote:

> Am I right to infer that currently BioPerl 1.6.x, like BioPerl 1.5.x  
> just
> treats the DE lines as only big long string?


> Could you translate your idea about the TagTree class into something
> concrete with BioSQL tables and fields for me? [...] Over on the  
> Biopython list we'd talked about storing this annotation in a nested  
> structured.

That's more or less what TagTree is.

>  However, in order to use the BioSQL annotations mechanisms, I think  
> a simple flat structure is required :(

Not necessarily. If you have a flat serialization (such as XML) the  
nested structure isn't needed. Of course that's not a fully normalized  
relational representation, but if you had one, how often would it be  
used, how efficient would those queries be (SQL is poor at nested or  
recursive data structures), and how much pain would it be to write the  
object-relational mappings?

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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