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Re: DTD/Schema for biological/biomedical datasets

  • To: <xml-dev@l...>
  • Subject: Re: DTD/Schema for biological/biomedical datasets
  • From: "Karen Harker" <Karen.Harker@U...>
  • Date: Fri, 18 Oct 2002 12:19:04 -0500

animal mouse schema
Thanks for the lead.  I looked at the documentation for both descriptions, but they seemed to concentrate too much on the physical descriptions of the human body (i.e. arm, leg, etc.).  Actually, very little research will be conducted on humans, so I've been looking at animal models (i.e. mouse, drosophila (mosquito), worms), but no luck there.
Thanks, again, and if you have any other ideas, I am more than willing to try them out.
Karen R. Harker, MLS
UT Southwestern Medical Library
5323 Harry Hines Blvd.
Dallas, TX  75390-9049

>>> Rex Brooks <rexb@s...> 10/17/02 6:40:10 PM >>>
Hi Karen,

The Human Markup Language being developed by the OASIS HumanMarkup TC (you can look it up on the OASIS website) will have a subset called the Human Physical Characteristics Description Markup Language which will intersect some of what you are looking for, and in a similar vein, will be including all the existing web, academic and medical standards, as well as coordinating with the Biometrics TC , which I have not followed closely because at the moment we are finishing up our Primary Base Schema and once we call for the 30-day public comment period, I will personally be switching over to the Physical Characteristics Description ML, probably early-mid-Novbember. If you remember you might want to look us up and contact me then. I would be happy to work with you on this.

Rex Brooks

At 4:39 PM -0500 10/17/02, Karen Harker wrote:
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: 8bit
Content-Description: HTML
I am a Web Developer/Librarian at UT Southwestern Medical Center Library in Dallas. The center will be conducting a large number of studies regarding bioterrorism in the near future (grant proposals are going out now) and I am considering proposing a project to provide a central repository for the datasets. 
We have just purchased a portal system (ENCompass) that organizes and searches resources using any DTD/Schema that is appropriate for that resource, and I would like to use that as the structure.  Since I don't want to re-invent the wheel, I would like to know if somebody is aware of a DTD or schema that has been developed for these objects, and if so, which would be the best to use.  The primary purpose I envision would be to store datasets (most likely after the data has been gathered, but before publication of results), easily find and download datasets based on such parameters as topics, objectives, hypotheses, animal models, exposures, etc., relate datasets with biomedical literature, and to share preliminary results with colleagues.
I am aware of a few DTDs, but I'm not sure if any would fit:
DDI - for social science & economic research
HDF5 - used by NCSA, but mostly on astrophysics
Tissue micro array DTD - uses DC, Gene Ontology, RDF, and  a self-referenced TMA - is particular to tissue slides.
Admittedly, I am only in the environmental scanning stage (who has done what) but I have not found much information. I would like to be more knowledgeable before I approach the big-wigs.
Thank you very much for your assistance.
Karen R. Harker, MLS
UT Southwestern Medical Library
5323 Harry Hines Blvd.
Dallas, TX  75390-9049

Rex Brooks
President, CEO, Starbourne Communications Design,
Executive Director, Humanmarkup.org, Inc.
Vice Chair, Secretary, Webmaster, OASIS HumanMarkup Technical Committee
Webmaster, OASIS Web Services for Interactive Applications Technical Committee


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