Bioperl: Bio* integration with AceDB

Ewan Birney
Fri, 16 Jun 2000 08:34:09 +0100 (GMT)

On Thu, 15 Jun 2000, David Block wrote:

> Reports from Acedb2000:
> A few of us met in the coffee room to discuss what needed to be/ could be
> done to better integrate with the Bio::* (Perl, Java, Corba, XML) effort.
> We came up with a few useful projects that need some volunteers to tackle
> them.  Of course, this also needs to be coordinated with the Bio* people.

Sounds great ;)

> Notes from the discussion:
> BioJava has been focussed on data processing, rather than UI.  They
> inherited AceDB client code.
> What is needed is an abstract data layer for objects that crosses
> boundaries.  BioCorba is using a common sequence definition derived from
> Bio::Perl.

Biocorba has a bioperl bias, but has been implemented by all three groups
(bioperl, biopython, biojava) though not heavily used. 

> Project:  Analyze the different sequence objects floating around and
> determine how to integrate them (there has to be a core of essential
> information that everyone is passing around).
> We then need a sequence transducer class (subclassed from Bio::SeqIO) that
> reads/writes Bio::Perl objects and .ace files and translates between them.

The Bio::SeqIO::ace would be great. Also viewing an AceDB as a
Bio::DB::SeqI (a sequence database) would also be great. If that was done
the "for free" you would get a biocorba server implemented in Perl , as
the bioperl corba server is written to work on top of the Bio::DB::SeqI 
interface (jason - feel free to correct me!)

> Project:  Create a SeqAlign object in Bio::Perl that reads homol sections
> from AceDB.

I don't think you want to make SeqAlign objects from AceDB homols, but
rather Bio::SeqFeature::FeaturePair objects.

> Project:  Using Bio::Perl blast parsing objects, store historical info/
> parameters/ essential results from blast hits in AceDB.  With Blast used
> for annotation, it would be helpful to have a way to reproduce the blast
> search and look at some of the primary data without having to store
> thousands of blast reports on your hard drive.
> Anyone interested, reply to me, or post to BioPerl.
> Dave Block
> NRC PBI Saskatoon
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420

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