[Genquire-dev] Re: mapping ensembl to Genquire (fwd)

[David Block]

David Block wrote:

> Maybe we're punting by using a higher-level screen.  Mark, what do you
> think?

I think we are being sensible by using a high-level screen ;-)

No, but seriously, I argue that biologists think in terms of contigs rather
than in terms of whole-chromosome coordinates... so why is it necessary to
load anything larger than a contig at any given time?  How often have you
*really* needed to scroll feature-by-feature over an entire human chromosome?
I can't say I ever have, nor will...

Besides which, genquire has a "forward" and "back" button to move you from one
contig to the previous/next in tiling-path order, so... what is the advantage
of having it all load up at once?

Punt!  (doesn't that mean 'drink' in England?)


> These are write-back questions, correct?  Mark and I stored GO things
> somewhat crudely and directly inside our TagValue table, using a small
> hack.  I'm not sure how we would want to handle this.

I think we should delay this decision while Ewan and Chris argue about "scary
DAG stuff".  Since Genquire tries to bind as tightly as possible to BioPerl,
the final decision on the structure of the annotation object will make a big
difference to the structure of our code (and our database probably...)


> We have had discussions about where annotations belong, on the gene or on
> the transcript.  The Genquire annotation code is part of
> GQ::Server::GenericFeature, so it can hang off of Genes, Transcripts, or
> Features (Exons, etc.).

and I like that!  Annotations at the exon level are de facto inherited by the
gene when that exon becomes part of a gene object.  It's nice... fortuitous...
but nice!


> BTW, it looks like I'm going to be spending some quality commuting time on
> a train here in California.  I look forward to some Ewan-ish outbursts in
> my future!

Sorry Dave, only British Rail results in creative outbursts.  Southern
California Rail leads only to massive perspiration.

M

--
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"Speed is subsittute fo accurancy."
________________________________

Dr. Mark Wilkinson
Bioinformatics Group
National Research Council of Canada
Plant Biotechnology Institute
110 Gymnasium Place
Saskatoon, SK
Canada