[Bioperl-l] bioperl-db revival

[Ewan Birney]

On Tue, 27 Mar 2001, David Block wrote:

> I've got most of this done already, on MySQL.  If you want to look, I can
> give you the code (it's part of WB2, which has been released free to
> non-profits).  If you take parts of it, great.

I'd love to have a look. I will be releasing this under the perl artistic
license if that makes a difference - I think putting weird license
restrictions on part of bioperl is a BadThing.

Send me the schema ... ;)

> 
> You would need to clean up the namespace,  (I could be helping with this),
> and the wrappers to Flybase/ensembl would be a welcome addition to my
> schema.  It outputs SeqI and SeqFeatureI compliant objects.
> 
> I use an inherited AUTOLOAD, which you don't like, I know, but combined
> with some fancy dynamic SQL generation, it lets you have
> 'entry-granularity mutability' for almost nothing in terms of coding or
> maintenance.  For things to behave properly, you need a compile time 'use'
> list of autoloaded subs, and a hash with the keys being the table columns.
> 
> It is all an evolved form of Damian Conway's example CD class in OOPerl,
> and it has been fairly stable for about six months.  I've only added on
> things that Workbench needs.
> 
> Anyone who wants a look, let me know.
> 
> -Dave
> 
> 
> 
> 
> 
> On Tue, 27 Mar 2001, Ewan Birney wrote:
> 
> > 
> > 
> > I have decided to revive bioperl-db for "simple" sequence storage.
> > 
> > [note to Hilmar/Jason - this is definitely the right place to put this now
> > I have written some of the SQL/code. It is completely bioperl dependent at
> > the moment. Our discussion about wider ranging infrastructure is
> > definitely worth keeping alive but this project is so dependent on bioperl
> > there's not much point in pretending otherwise]
> > 
> > 
> > The aim is a pretty vanilla set of SQL tables, quite normalised, nothing
> > fancy. The only sticking point are the dreaded feature locations, which,
> > if we go the full fuzzy modelling (aaaaarh not the fuzzies again) I
> > will need help (jason - can you face the fuzzies again?). 
> > 
> > At the moment I am going to have a cheeky "unparsed_location" string table
> > for the fuzzies.
> > 
> > 
> > To bind to the SQL tables I will have a series of pretty vanilla
> > "adaptors" talking Ensembl or FlyBase, equivalent I believe to Java Bean
> > singleton objects talking java (? java experts to correct me) which
> > mediate persistence of Bio::Seq objects.
> > 
> > The only wrinkle here is how to deal/detect nicely one-instance style
> > objects, such as Species (homo sapiens). I will I hope glean some wisdom
> > from Arne Stabenau on this tomorrow but if anyone has some helpful ideas,
> > just put them down here.
> > 
> > 
> > For output, it will definitely support appropiate Bio::DB:: *I interfaces
> > and probably extend it for simple field orientated queries that can be
> > easily mapped to SQL (nothing fancy)
> > 
> > 
> > For input it will have a loader script that can load a SeqIO stream into
> > the database.
> > 
> > 
> > It will be able to support mutliple logical "databases" (eg, swissprot and
> > genbank) in the same db instance and handle multiple versions of
> > sequences. It will not currently handle true entry-granualarity
> > mutability, but if anyone has any must-do-now aspects please shout.
> > 
> > 
> > I want to put code in the Bio::DBSQL:: namespace. Is this ok?
> > 
> > 
> > Code will go into the bioperl-db cvs module
> > 
> > 
> > I have a tight-ish deadline on this, so please shout if you feel you want
> > to add anything.
> > 
> > 
> > 
> > 
> > 
> > ewan
> > 
> > 
> > 
> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> -- 
> David Block
> dblock@gene.pbi.nrc.ca
> http://bioinfo.pbi.nrc.ca/dblock/wiki
> Plant Biotechnology Institute
> National Research Council of Canada
> Saskatoon, Saskatchewan
> 
> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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