[Bioperl-l] module proposal Bio::DB::PDB

[Steve Chervitz]

I don't like the name "StructureDBI" because people may think it is somehow
related to DBI.pm (e.g., a subclass). Bio::DB::StructureDatabaseI and
Bio::DB::SeqDatabaseI would avoid this problem.

How's ISMB going? Any breaking news?

Steve

--- Hilmar Lapp <hlapp@gnf.org> wrote:
> I agree. The name of the generic interface should maybe better be 
> Bio::DB::StructureDBI, or Bio::DB::RandomAccessStructureI. This BTW 
> also tells us that Bio::DB::RandomAccessI isn't the best name; it 
> should rather be Bio::DB::SeqDBI or Bio::DB::RandonAccessSeqI for 
> consistency ...
> 
> Just my Can$0.02 (still at ISMB).
> 
> 	-hilmar
> 
> On Tuesday, August 6, 2002, at 03:27  AM, Ewan Birney wrote:
> 
> > On Tue, 6 Aug 2002 lsprilus@bioinformatics.weizmann.ac.il wrote:
> >
> >> Hi,
> >>
> >> We are considering to develop a Bio::DB::PDB module for allowing 
> >> access
> >> (search, retrieval, analysis) to OCA and PDB databases.
> >
> > I would suggest setting up an abstract interface with methods like:
> >
> >    $db->get_Structure_by_id();
> >
> >    $query = $db->get_Structure_by_query($string);
> >
> >    where $query has methods ->next_structure, like StructureIO
> >
> > (Lincoln and others - should we stick to the convention 
> > get_XXXX_by_YYYY?)
> >
> >
> > Then PDB and OCA databases (don't known what OCA is!) are 
> > implementations
> > of Bio::DB::StructureI (ie, Bio::DB::PDB implements 
> > Bio::DB::StructureI)
> >
> >
> >
> >
> >>
> >> I would appreciate comments and suggestions.
> >>
> >> Jaim
> >> --
> >>  Dr Jaime Prilusky                | Jaime.Prilusky@weizmann.ac.il
> >>  Weizmann Institute of Science    | fax: 972-8-9344113
> >>  76100 Rehovot - Israel           | tel: 972-8-9344959
> >>
> >>  info URL http://bioinformatics.weizmann.ac.il/jaime_prilusky.html
> >>  OCA is at http://bioinformatics.weizmann.ac.il:8500
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l@bioperl.org
> >> http://bioperl.org/mailman/listinfo/bioperl-l
> >>
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l


=====
Steve Chervitz
sac@bioperl.org

__________________________________________________
Do You Yahoo!?
Yahoo! Health - Feel better, live better
http://health.yahoo.com