Re: ontology specs for self-publishing experiment

[William Bug]

On Jul 6, 2006, at 12:55 PM, William Bug wrote: In the context of the comment above, this is being addressed by trying to establish a foundational ontology for biomedical reality and an ontology of relations ([]).  I realize we went through this debate of the foundational ontology a few weeks back, but a fairly specific path is already being followed by the folks working on the OBO Foundry Ooops. In my haste, juggling this with 3 other parallel tasks in the lab this afternoon, I missed the references here, though I expect many on this list are aware of what I'm referring to. Relations in biomedical ontologies Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kumar, Jane Lomax, Chris Mungall, Fabian Neuhaus, Alan L Rector  and Cornelius Rosse Genome Biology 2005, 6:R46     doi:10.1186/gb-2005-6-5-r46 http://genomebiology.com/2005/6/5/R46 Basic Formal Ontology (SNAP/SPAN) http://ontology.buffalo.edu/bfo/ Biodynamic Ontology http://ontology.buffalo.edu/medo/biodynamic.pdf The Ontology of Biomedical Reality http://ontology.buffalo.edu/medo/biomedo.htm Please note the unifying factor for all of the above - beyond the formalisms presented - is Dr. Barry Smith (http://ontology.buffalo.edu/smith/). Despite the debates that continue on this topic, over the past 2 years, this body of work has had a very powerful influence over a wide swarth of work in large-scale, field-wide, biomedical KR/KD, so it's worth keeping it on our radar. I would stress this influence extends well beyond the realm of creating explicit, formal ontological frameworks to support complex, automated reasoning but is targeting much more basic levels of formal semantic representation - such as semantically-based, biomedical data integration - I believe to be directly relevant to several of the discussion threads across the W3C SW HCLSIG lists. Cheers, Bill Bill Bug Senior Analyst/Ontological Engineer Laboratory for Bioimaging  & Anatomical Informatics www.neuroterrain.org Department of Neurobiology & Anatomy Drexel University College of Medicine 2900 Queen Lane Philadelphia, PA    19129 215 991 8430 (ph) 610 457 0443 (mobile) 215 843 9367 (fax) Please Note: I now have a new email - [EMAIL PROTECTED] This email and any accompanying attachments are confidential. This information is intended solely for the use of the individual to whom it is addressed. Any review, disclosure, copying, distribution, or use of this email communication by others is strictly prohibited. If you are not the intended recipient please notify us immediately by returning this message to the sender and delete all copies. Thank you for your cooperation.