[Bioperl-l] Unigene proposal and basic implementation

[JDiggans@genelogic.com]

> Just an aside - we might want to be more specific with the
> ClusterI name - like Seq::ClusterI so that we don't confuse
> people with the potential GeneExpression Expression::ClusterI
> one day.  But that can be up for debate if others want to
> throw it in the root of Bio::.

Wanted to voice my support for the Seq::ClusterI route ... I'd definitely
eventually like to see bioperl branch out into the realm of gene expression
(and metabonomics, proteomics, whatevercomesnext-omics, blah blah) and
since clustering can mean different things to different people in different
contexts we should be as specific as possible.

To play catch up, is the current seq cluster design something like:

Seq::ClusterI
  |
  |---> Seq::Cluster (?)
  |
  |---> Seq::Cluster::UnigeneI
    |
    |---> Seq::Cluster::Unigene
  |
  |---> Seq::Cluster::GenericESTClusterI
    |
    |---> Seq::Cluster::GenericESTCluster


> it will be a collection of sequences (or sequence references --
> accessions) which will likely share a common set of annotations

I'd definitely be for not getting too Unigene-focused ... the base
Seq::ClusterI shouldn't be too much more than a collection of sequences (or
references to sequences) and accessor methods to get/set those sequences
(plus perhaps a ClusterIO layer?). A cluster of sequences doesn't even
necessarily need to share any sequenced-based annotation so we should be
careful to define what we mean by a 'common set of annotations'. The
annotation could be something random like 'regulated in X disease' ... I
haven't worked at all w/ the AnnotationCollectionI stuff so perhaps this
abstraction is already taken care of there by giving a Cluster an
AnnotationCollection.

> Of course I just expanded the SearchIO.t to 539 tests...

Yowsa.
-j

-------------------------------------------------
James Diggans
Bioinformatics Programmer
Gene Logic, Inc.
Phone: 301.987.1756
FAX: 301.987.1701