Bioperl: fixed bug #226

Hilmar Lapp
Sun, 07 May 2000 15:54:55 +0200

Ewan Birney wrote:
> Hmmm. I am worried that for species that do not have a subspecies
> identifier that we will falsely classify the subspecies as a species.
> Can you reassure me that this wont happen?

I hope the doc could. The test script actually contains the example quoted
from the doc, and it prints "ok" on my machine. Anyway, if it fails somewhere,
we'll hear about it.

> > Regarding design, I have the impression that Bio::Species rather encapsulates
> > the source of a sequence (therefore the organelle() method) than a species
> > only, and that's exactly the point of interest with respect to seqs (like
> > organ, tissue, library etc). So, intuitively I'd call it something like
> > Bio::SeqSource or Bio::IsolationSource. Does anyone see a point in this? I
> > have no idea how much attention the list community pays to such issues, so
> > maybe someone can give me an idea whether this is just stupid and you leave
> > such things to the OO/Corba/Java domain.
> >
> I think the species object should handle biologically species *only*.
> issues like organelle are half way split between species issues and source
> issues - I could argue it either way. In my view, a good design is
> something like
>   Bio::IsolationSource has-a Bio::Species object
> and also has additional methods for tissue etc.

Agreed. This is similar to like it is modeled in a database we have developed,
and I guess also to DBs used or developed at EBI, like the Expression
Database. Maybe one should simply use their design as a guideline, in order to
avoid duplicating the according discussion, although discussing things again
is generally not bad thing.

> I refuse to let the bioperl object model be dominated by EMBL/GenBank
> parsing issues. It is an evolutionary dead-end in my view.




Hilmar Lapp                                      email:
NFI Vienna, IFD/Bioinformatics                   phone: +43 1 86634 631
A-1235 Vienna                                      fax: +43 1 86634 727
ROI: Bioinformatics (arrays, expression, seqs), Programming, Databases,
     Mountain Biking (hard tail, hard fork: feel the trail)
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