[MOBY-l] Nucleotide as an attribute of Sequence?

[Mark Wilkinson]

Hi Boris! (and Lukas, and Midori)

> Ie.: is "nucleotide" an attribute to a sequence object or is
> "nucleotide-sequence" an object in it's own right ?

To be honest, I'm a bit confused by the object hierarchy that Lukas submitted to the
CVS.  Lukas, perhaps you can weigh in on this conversation and clarify some things?

In my interpretation (which is probably out to lunch) there is a VirtualSequence,
which simply has a Length attribute.  There are then 5 objects which inherit from
VirtualSequence:

        Sequence - which contains an actual sequence (apparently DNA, Protein, or
other)
        DNA - which has many sub-objects inheriting from it
        RNA - which has sub objects
        Protein - gives birth to ProteinSecondaryStructure
        Domain - with children

What confuses me is why DNA doesn't inherit from Sequence, rather than being at the
same level as.  Is this a typo?  I don't think it is a typo because SequenceFragment
seems to also have a sequence attribute...  This is another issue that came up
yesterday as I was building the basic retrieve service - it will send back
either/both DNA or AA sequences depending on the accession number it is given, so
the Sequence object was not really sufficient for this purpose unless it had
DNA/RNA/Protein children.

I'm also concerned about EST being a child of RNA  ;-)  ... but that's another
story.

Midori - are you already using a tool to edit these hierarchies?  Are you back from
your trip?  If you already have a fancy editing system perhaps we should all install
it so that we can browse/edit more easily, and if possible have a flat-file in the
CVS as you have already done for the Service hierarchy (thanks!).  Are you using
GOAT?

Lukas, perhaps a telephone call would be helpful in clarifying some of these
things?  Tell me what time is best for you and I'll call.

Cheers!

Mark


--
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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