[humanmarkup] Physiome

[Rex Brooks <rexb@starbourne.com>]

Hi Everyone,

My preliminary research into Physiome shows that it has evolved into
a drug research company more than anything else, despite the
Scientific Advisors who are all luminaries, and quite well-connected.
However, while we may want to contact some of those individuals to
see what the remaining connection to AnatML is, I think it would be
unwise to attempt to associate our effort with any proprietary
concerns until they seek to join us after we have established the
validity of our work. At that time, after we have our first TC spec
submitted for approval, we may wish to consider contacting this
company, but for now I think we should confine our attempts at
contact to individuals who may best be thought of only as advisors to
this company.

A search of their site on AnatML revealed:

Physiome Sciences and researchers at the University of
Auckland, New Zealand, have launched the CellML
website (www.CellML.org) to provide a tool for researchers
to standardize and streamline the creation of
computer-based models of cells, organs and tissues.

CellML is an XML-based mark-up language designed to
facilitate the creation and exchange of biological models.
CellML allows users to share models even if they are
using different model-building software. It also lets them
reuse components from one model in another, thus
accelerating model-building..

CellML is expected to enable scientists to more
effectively manage and interpret gene and protein data
and apply it to study diseases, identify potential drug
targets and test new drugs "in silico." The language will
be developed as a common standard that will be available free of
charge to all users.

CellML is a collaborative effort between Physiome Sciences and the
University of Auckland to
develop and maintain a family of Physiome Mark-up Languages that also
include AnatML and
FieldML for describing anatomic data and the spatial distribution of
biological properties

So, we still don't know much about AnatML, and the home page of the project:

http://www.esc.auckland.ac.nz/sites/physiome/anatml/pages/

remains unchanged since I visited it last and contains no new
information since April 2000, when Physiome was still a Project at
Princeton.

This brings up an interesting point, and one I think we need to
consider, and that is whether or not we wish to require our
specification to be harmonized only with existing, maintained,
sources? I have not come to any conclusion myself, and if the AnatML
is not being actively maintained, and we think it is valuable, we may
want to see if NIST would consider adopting it.

Ciao,
Rex
--
Rex Brooks
Starbourne Communications Design
1361-A Addison, Berkeley, CA 94702 *510-849-2309
http://www.starbourne.com * rexb@starbourne.com