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Re: BioRDF [Telcon]

From: William Bug <William.Bug@DrexelMed.edu>
Date: Mon, 8 Jan 2007 14:07:41 -0500
Message-Id: <5D976355-4C34-4A52-A06B-457B2B21558C@DrexelMed.edu>
Cc: Susie Stephens <susie.stephens@oracle.com>, 'public-semweb-lifesci' <public-semweb-lifesci@w3.org>
To: Kei Cheung <kei.cheung@yale.edu>
Very much so, Kei.  Thanks for bringing this up.

Maryann Martone, Jeff Grethe, myself, and others involved in the  
Bioimaging contingent contributing to the Ontology of Biomedical  
Investigation (designed to cover experiment assays, equipment,  
reagents, etc.) have spent some time looking at OME.  There have been  
discussions regarding what portions of their work represents data  
modeling syntax and what portions represent semantics.  Right now, I  
don't believe OME makes a significant distinction between the two.   
Regardless - there is a considerable amount of valuable structured  
semantics contained within OME.

Another important imaging ontology - one that can be of significant  
use when describing imaging experiments - is the EBI Flybase  
Bioimaging methods ontology (FBbi - http://www.ebi.ac.uk/ontology- 
lookup/ontologyList.do).  This started very focussed on the sort of  
in situ and whole-mount imaging specific to Drosophila work but has  
really matured considerably in the last year.  In particular, it's  
very good for capturing the detail associated with histological  
techniques used in various forms of light microscopy - an EXTREMELY  
important aspect that must be captured semantically, if we have any  
hope of integrating analyses and assertions based on separate imaging  
experiments.

There is a need to deal more with methods associated with  
radiological imaging of various sorts - an issue that - as Daniel  
mentioned - is being address by the imaging task force in caBIG, by  
BIRN, and by a few other efforts.  OME & FBbi both focus almost  
exclusively on light microscopy.  Maryann Martone - co-chair of the  
BIRN OTF - and a neuroanatomist with extensive experience using  
ultrastructural imaging is also working on electron microscopy as a  
part of the BIRNLex framework.

Ultimately, all of this need to integrate with - and/or derive from -  
OBI.

Cheers,
Bill


On Jan 8, 2007, at 1:39 PM, Kei Cheung wrote:

>
> Hi All,
>
> I just wonder if the Open Microscopy Environment standard described  
> in the following article is applicable to semantic annotation of   
> neuroimages.
>
> http://cdp.mit.edu/pdf/Goldberg-15892875-2005.pdf
>
> Best,
>
> -Kei
>
>
> Susie Stephens wrote:
>
>>
>> Here's a reminder for Monday's BioRDF call.
>>
>> Date of Call: Monday January 8, 2007
>> Time of Call: 11:00am Eastern Time
>> Dial-In #: +1.617.761.6200 (Cambridge, MA)
>> Participant Access Code: 246733 ("BIORDF")
>> IRC Channel: irc.w3.org port 6665 channel #BioRDF
>> Duration: ~1 hour
>>
>> Agenda
>> - Review action items.
>> - Kei Cheung will provide a status update regarding the BMC  
>> Bioinformatics paper.
>> - Daniel Rubin will highlight the use of images within scientific  
>> queries.
>> - Bill Bug will describe some of the most appropriate use cases  
>> from BIRN.
>> - Finalize decisions regarding the best venue for the demo.
>> - AOB.
>>
>>
>>
>
>
>

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





Received on Monday, 8 January 2007 19:08:03 UTC

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