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Subject: Re: Competing Anatomy Specifications, Ontologies, XMLVocabulariesand Data Dictionaries


Title: Re: Competing Anatomy Specifications, Ontologies, XML
Thanks so much, Peter,

Between your reply and Prof. Rosse's, I believe I now have a much firmer grasp of how these two efforts fit together and a good idea that these two efforts are both public domain, and therefore completely useable. This is good news indeed. I agree that the ontological issues are extremely important, and, in fact, I even compiled one for us more than a year ago, to get an idea out of what our reference frameworks would be. We have since set the ontological issue aside as we worked on our Primary Base Specification. It now appears, as I approach the work of the HPCDML Subcommittee, that an ontological framework and RDF Schema will be among the first tasks we address as we start work on a Requirements Document to follow our charter and mission.

Thanks again, and I can't express what a relief this is, since I would much rather not attempt to cope without both of these resources.

Regards,
Rex
At 10:13 AM +1200 4/29/03, Peter Hunter wrote:
Dear Rex,
Thanks for the email - it's great to see the OASIS effort underway on HumanML.  I would like to comment on your statement/query re the commercial links for AnatML.
1. AnatML has always been a public domain effort with no commercial funding. We have been developing anatomically based computational models of various organ sytems at the University of Auckland for over 20 years and have always made them freely available (our heart models, for example, are used by many cardiac research groups around the world). Software for viewing the 3D models is freely available from www.cmiss.org.
2. About six years ago we started developing an XML markup language for modelling cellular processes, which we called CellML. A year or so after we began this effort we obtained some funding for this project from a US company called Physiome Sciences Inc. This funding finished last year - Physiome always supported it as a public domain effort and only intended to fund us until public domain funding could take over. The project is now funded entirely by the New Zealand Government via the NZ Royal Society. It has always been a public domain project and source code is freely available to anyone (i.e. academic and business) via the cellml.sourceforge.net site.
3. The reason for the apparent hiatus in Anatml development is that we decided to address ontology issues before providing public access to all our anatomical models (i.e. we need the ontologies as a means of accessing the models). This turned out to be a much bigger can of worms than we had anticipated and of course we discovered that many other groups have similar ambitions so we have teamed up with them - see http://www.sofg.org/species/human.html. The SOFG effort is being led by Duncan Davidson in Edinburgh.
4. In 2001 I was appointed Chair of the Physiome Commission of IUPS (the International Union of Physiological Sciences) - which belongs to ICSU (the International Council of Scientific Unions) - and in that role I am leading the IUPS Physiome Project (see http://www.bioeng.auckland.ac.nz/physiome/physiome.php).
5. It is clearly extremely important that ontologies are developed with a very wide user support base. The Digital Anatomist project led by Cornelius Rosse is the most comprehensive effort so far at the large scale anatomy level and the Gene Ontology (GO - see www.geneontology.org) is the most comprehensive effort at the gene/protein level. 

Hope this helps.
Best wishes,
          Peter
 
Rex Brooks wrote:
Hi Folks, Since I wrote to Dr. Cornelius Rosse more than a week ago now, April 19, I think it will be acceptable that I simply include our interest in his work with the Digital Anatomist Foundational Model within the University of Washington School of Medicine in this message. My inquiry into the Protege-Readable Anatomical Ontology is part of my exploration of accepted human anatomy specifications, standards, ontologies, data dictionaries, and references commonly used or required in medicine, public health and safety and various levels of government from local to state or province to national and/or international. I am now attempting to cover all of my bases when I ask for all relevant references and inputs for the work of the OASIS HumanMarkup Technical Committee, Human Physical Characteristics Description Markup Language (HPCDML) Subcommittee. The Charter and Mission Statement for this subcommittee is currently in the process of a vote to approve it by the Technical Committee, so I am attaching it in two versions, Word and rtf with the proviso that it is unofficial as of 28 April 2003. The subcommittee is also in the process of formal inauguration within the new OASIS structural system. However, I can assure you that I expect that it will be approved and duly adopted and that the subcommittee will begin its formal work soon. My concern is that there appear to be competing ontologies and standardized markup vocabularies or language standard efforts working on this vital and necessary endeavor. So, since my aim is to harmonize and ensure interoperability of the existing accepted standards, I am seeking aid in my work to identify such standards and ongoing efforts aimed at constructing such standards. In this particular context, I am seeking guidance on obtaining all relevant to ANATML (of which I was apprised more than a year ago, but which had appeared to be moribund until recently, and is closely related to a for-profit corporation which may make it less attractive or perhaps unavailable for use in an open, public, royalty-free standard) http://www.physiome.org.nz/sites/physiome/anatml/pages/index.html and The Digital Anatomist Foundational Model http://sig.biostr.washington.edu/projects/fm/AboutFM.html and their value in relation to each other and the overall field described in the charter/mission document attached. Since the Digital Anatomist is unavailable to the public, I can't compare it to ANATML. ANATML is dated 2000, and consists of a DTD, which is usable, but its relation to a for-profit corporation, despite being developed The University of Auckland, NZ, makes it uncertain for our use. These appear to be the two candidates for the more purely anatomical interests of our subcommittee, and I want to emphasize that anatomy is just one of a set of issues with which HPCDML will be concerned. I will be more than pleased to send to this set of addrressees the paper on the body of standards and specifications the HPCDML identifies as required for coverage within its charter when we decide that we have researched this area sufficiently for a first draft of a requirements document for the subcommittee. Thanks very much, and I do hope this is not an intrusion. Regards,Rex
--
Rex Brooks
President, Stabourne Communications Design
Executive Director, Humanmarkup.org, Inc.
Vice Chair, Secretary, OASIS HumanMarkup Technical Committee
Chair OASIS Human Physical Characteristics Description Markup Language Subcommittee
Member Web Services for Interactive Applications Technical Committee
Chair Web Services for Remote Portal Markup Subcommittee
Member OASIS Emergency Management Technical CommitteeGeoAddress: 1361-A Addison, Berkeley, CA, 94702 USA, Earth
W3Address: http://www.starbourne.com
Email: rexb@starbourne.com
Tel: 510-849-2309
Fax: By Request


-- 
Rex Brooks
GeoAddress: 1361-A Addison, Berkeley, CA, 94702 USA, Earth
W3Address: http://www.starbourne.com
Email: rexb@starbourne.com
Tel: 510-849-2309
Fax: By Request


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