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RE: SemWeb BOF @ ISMB 04

From: wangxiao <wangxiao@musc.edu>
Date: Mon, 26 Jul 2004 23:48:34 -0400
Message-Id: <200407270348.i6R3mSrA009920@flopsy.musc.edu>
To: <public-semweb-lifesci@w3.org>

Greeting all:

I am glad to see this lifesci thread getting life now :-).  

I believe one of the main problem in life science is the same as the
original problem that Eric Neumann has posted.  That is how to refer part of
non-RDF document.  

I am working on a project aimed at using RDF to represent 2D-Gel data.  I
understood why Mr. Peter Murray-Rust did not accept Tim Berners-Lee's
suggestion to create a CML ontology because I have the same concern of
overhead for using either RDF or XML to represent Gel data as well.  In my
cases, my concern is this.  For some applications, such as data submission
and retrieval, I actually wanted the gel encoded in a "compact" form.
Personally, I don't think XML is a good solution because there are more
overhead than the actual payload.  Neither will RDF a good solution for the
same reason.  It is not that difficult to create an arbitrary format to
encode the gel data in a compact text based format but then I don't know how
the URI should be assigned to each individual spot.  The URI for the spot is
important because if a spot is IDed or used to perform MS.  The URI can make
it easy to associate other type of descriptions. 

I guess this problem - assigning URI to part of another resource -  is more
general than it is just the life science alone. I would be very glad to hear
if your "BDF" meeting can get some good solution.

By the way, I think RDF lacks a graphical modelling language like UML.  One
of the main RDF activities will be designing ontologies.  So, a graphical
language sort of like UML will be very useful during the design phase and
for the purpose of discussion and presentation.  I don't think UML is
suitable to presenting RDF/OWL and I goggled internet but didn't find any
useful one. I therefore created one.  It helps me and it might be of useful
to you too.  An introduction of the language, which I called DLG2, is at
http://bioinformatics.musc.edu/cc/tools/dlg2/
and a detailed documentation is at
http://bioinformatics.musc.edu/cc/docs/dlg2/dlg2.htm.  Please note, I just
started writing these document.  There must be many problems.  Please
forgive my careless writing and any suggestions and criticism are welcome!

Also, our project - Charleston Core (http://bioinformatics.musc.edu/cc/) is
similar Eric Jain's but focuses on proteomic data.  If any of you have
suggestion or want to collaborate, please feel free to contact me.

Xiaoshu Wang
Received on Monday, 26 July 2004 23:49:10 GMT

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