Re: Martone's Ontology

Sounds like a good idea to me.

I'll try to spend some time going back-n-forth with Don over the  
weekend to create the list of relevant ontologies, terminologies, and  
classification schemes relevant to the Use Cases.  That will help to  
give us a point of reference.  I'll also look through writeups from  
the BioRDF folks, to get a sense of the entirety of formal resources  
they've worked with.  I know the usual suspects, but I'll try to cull  
some sense of what they think regarding how effective they turned out  
to be in representing the facts they had to cover.

Cheers,
Bill

On Jan 11, 2007, at 7:43 PM, Kashyap, Vipul wrote:

> If it makes sense, we could put it on the agenda item for the next  
> BIONT Telcon?
>
>
>
> ---Vipul
>
>
>
> From: William Bug [mailto:William.Bug@DrexelMed.edu]
> Sent: Thursday, January 11, 2007 6:05 PM
> To: Kashyap, Vipul
> Cc: Donald Doherty; public-semweb-lifesci
> Subject: Re: Martone's Ontology
>
>
>
> By the way, while we're on the topic, there's another very useful  
> ontology which we certainly want to have on our list of relevant  
> ontologies.  It addresses some of the issues directly relevant to  
> both Use Cases and the issue Don brought up at the start of this  
> thread - "describing distributions or receptors on a cell,  
> locations of various processes in a cell" - in this case, for  
> neuronal synapses.
>
>
>
> SynDB: a Synapse protein DataBase based on synapse ontology.
>
>           http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? 
> db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17098931&query_hl=1 
> &itool=pubmed_docsum
>
>
>
> Again - as I mentioned before, we also want to review this issue  
> with the BioRDF folks - e.g., confer with Kei on his sense of what  
> relevant TBox structure is provided in the SenseLab resource - and  
> we should definitely review this issue with Matthias.
>
>
>
> Cheers,
>
> Bill
>
>
>
> On Jan 11, 2007, at 3:50 PM, Kashyap, Vipul wrote:
>
>
>
>
> Do you mean create a page on the BioONT Wiki where we list  URLs  
> pointing to the OWL files for these ontologies for anyone to view  
> in their favorite OWL editor?  We probably have that already, right?
>
> [VK] Actually, we don’t and that would be a good idea as well!
>
>
>
> Would you rather have the content of the ontologies set up on a  
> page we can comment on?  That's not so easy to do, though for SAO  
> and for the BIRNLex ontology, I'd be able to get us access to  
> OWLDoc versions folks could easily navigate through in a web browser.
>
> [VK] That would be a better and more “readable” idea…. Might be as  
> simple as taking at text non-xml version of the OWL ontologies…
>
>        We sort of need to start building up a collection of  
> ontologies and data sources as we start building up the use cases…
>
>
>
> Just thinking aloud… Feel free to suggest alternate configurations.
>
>
>
> ---Vipul
>
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>
>
> 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
>
>
>
>
>
>
>
>
>
>
> THE INFORMATION TRANSMITTED IN THIS ELECTRONIC COMMUNICATION IS  
> INTENDED ONLY FOR THE PERSON OR ENTITY TO WHOM IT IS ADDRESSED AND  
> MAY CONTAIN CONFIDENTIAL AND/OR PRIVILEGED MATERIAL. ANY REVIEW,  
> RETRANSMISSION, DISSEMINATION OR OTHER USE OF OR TAKING OF ANY  
> ACTION IN RELIANCE UPON, THIS INFORMATION BY PERSONS OR ENTITIES  
> OTHER THAN THE INTENDED RECIPIENT IS PROHIBITED. IF YOU RECEIVED  
> THIS INFORMATION IN ERROR, PLEASE CONTACT THE SENDER AND THE  
> PRIVACY OFFICER, AND PROPERLY DISPOSE OF THIS INFORMATION.

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