[Pipet Devel] Re: Comment on Re: The Loci Project

[J.W. Bizzaro]

Paul Gordon wrote:
>
> IMHO:
> It's a nice concept, but I think it misses a strong point of BIOML and
> BSML.  Mozilla and IE can display the sequence with your mixed markup, but
> what can you actually *do* with the data?  Form and display is provided,
> but without an extensive standard markup there isn't much activity
> related to the sequence (such as visualization and feature hightlighting
> for example of annotated sequence) that the browser can provide to the
> user.
> 
> A very small DTD would provide little benefit over straight HTML. If you
> just want to exchange DNA, RNA or protein between applications, FASTA is a
> pretty simple, common format.

With Loci, we are toying with the idea of giving every bio-object, as defined
via XML, a unique identification number.  This way objects can refer to one
another without being necessarily nested, one inside the other.  This allows for
various, small XML's to be used, even XML's that are unrelated.

For example, we intend to use XML for graphics.  Should we then define one DTD
to represent all biodata plus all graphics?  We could, but it would be more
practical to break it up.  How about phylogenetics?  It's not completely
compatible with say molecule structure information, and the user will likely
care about only one or the other.  So should phylogenetics and structure always
be used together?  What about polysaccharide sequence and structure?  That's
such a new area but every bit as much a part of biology as DNA sequence.  Should
the completion of a DTD be held off until every aspect of biology is
understood?  Should there be one big DTD that has to be changed with every new
issue of a scientific journal?

Of course Loci is not really concerned with Web representations, so I'm not
addressing those issues.


:-)
Jeff
-- 
J.W. Bizzaro                  mailto:bizzaro at bc.edu
Boston College Chemistry      http://www.uml.edu/Dept/Chem/Bizzaro/
--