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

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 - William.Bug@DrexelMed.edu







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