Re: [BIONT] Latest Version of Parkinson's Disease Ontology (Molecular and Cellular Viewpoint)

[William Bug]

Hi All, As a quick follow-up to our discussion of foundational ontologies at play here, here a few URLs.  By the way, I left out a very import one we should be looking to use where ever it fits our needs. That's the OBO Relations ontology. I will add the following to a BIOONT Wiki page on foundational biomedical ontologies, along with a very few pertinent citations as Alan suggested - just enough to acquaint us all with the relevant arguments.  Please feel free to augment this list, if you believe I've missed something import.  From what we create on this page, we will definitely be able to establish a small collection of critical resources on this topic from which we can all draw. As Alan mentioned, a lot of the issues discussed in these citations are non-intuitive depending on your background, so it can require significant review before you absorb the subtleties - at least that was what I found I needed to do.  ;-)   I expect this is a fact many on this list have already confronted. Cheers, Bill Basic Formal Ontology (IFOMIS - Barry Smith, Pierre Grenon, et al.) OWL URL (Many many thanks to Holger Stenzhorn for putting out a concrete first draft for review): http://www.ifomis.uni-saarland.de/bfo/1.0/ Documentation: http://www.ifomis.uni-saarland.de/bfo/ (recently re-organized in a way that helps give a clear since of what BFO is and where it is currently being used) related citations (on application of BFO in the biomedical domain): Ontology of Biomedical Reality: http://ontology.buffalo.edu/medo/biomedo.htm Biodynamic Ontology http://ontology.buffalo.edu/medo/biodynamic.pdf [currently amongst the OBO Foundry ontologies, FMA (and the less species specific Common Anatomy Reference Ontology) and OBI (formerly FuGO) are making heavy use of BFO and is currently being refactored to import BFO classes as opposed to having hard-coded them directly into OBI.  We are doing the same with the BIRNLex BIRN ontology, as are other community-developed ontology projects] Simple Bio Upper Ontology (Alan Rector, Robert Stevens, Jeremy Rogers) - GALEN foundations + DOLCE elements + FMA elements (some insight from BFO) basic info: http://www.cs.man.ac.uk/~rector/ontologies/simple-top-bio/ Citations: "A Simple Upper Level Ontology in OWL for Biomedicine" (http://www.cs.man.ac.uk/~rector/ontologies/simple-top-bio/PSB-poster.pdf#search=%22simple%20bio%20upper%20ontology%20rector%22) "Modularisation of domain ontologies implemented in description logicsand related formalisms including OWL" (http://www.cs.man.ac.uk/%7Erector/papers/rector-modularisation-kcap-2003-distrib.pdf) OBO Relations Ontology URL: http://obo.sourceforge.net/relationship/ OWL-Full: http://obo.sourceforge.net/relationship/relationship.owl Citation: "Relations in Biomedical Ontologies" (http://genomebiology.com/2005/6/5/R46) GENIA - Upper Level Ontology for Molecular Biology (Udo Hahn, Stefan Schulz, Elena Beisswanger, Joachim Wermter) Citations: "Towards An Upper Level Ontology for Molecular Biology" (http://supreme.coling.uni-jena.de/BootStrep/bin/viewfile/Extern/PublicationPage?rev=;filename=Towards_an_Upper-Level_Ontology_for_Molecular_Biology_-_AMIA2006.pdf#search=%22simple%20bio%20upper%20ontology%20rector%22) Cheers, Bill On Sep 19, 2006, at 9:22 AM, Kashyap, Vipul wrote: In preparation of the BIONT Telecon today,   The latest version of the Parkinson’s Disease Ontology in OWL is available at: http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/ OWL-DL axioms that model some of the “facts” identified by Bill Bug are available at the bottom of:http://esw.w3.org/topic/HCLS/OntologyTaskForce/SeedOntology/SeedOntologyDetailedFollowup   Look forward to feedback and comments.   ---Vipul   ======================================= Vipul Kashyap, Ph.D. Senior Medical Informatician Clinical Informatics R&D, Partners HealthCare System Phone: (781)416-9254 Cell: (617)943-7120 http://www.partners.org/cird/AboutUs.asp?cBox=Staff&stAb=vik   To keep up you need the right answers; to get ahead you need the right questions ---John Browning and Spencer Reiss, Wired 6.04.95   Bill Bug Senior Research 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.