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Martone's Ontology

From: Donald Doherty <donald.doherty@brainstage.com>
Date: Thu, 11 Jan 2007 10:42:17 -0500
To: "'William Bug'" <William.Bug@DrexelMed.edu>
Cc: "'public-semweb-lifesci'" <public-semweb-lifesci@w3.org>
Message-ID: <006001c73597$151aa4f0$2f01a8c0@Brainstage>
Hi Bill,

 

At Neurosciences Maryann Martone talked about her ontology being nearly
ready for public consumption. (I forgot the name of her ontology.) It
sounded like it would be very helpful in situations like describing
distributions or receptors on a cell, locations of various processes in a
cell, etc.

 

Am I correct on the types of uses it's meant for? Is there any news on the
ontology's availability?

 

Don

 

-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of William Bug
Sent: Monday, January 08, 2007 2:08 PM
To: Kei Cheung
Cc: Susie Stephens; 'public-semweb-lifesci'
Subject: Re: BioRDF [Telcon]

 

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 Thursday, 11 January 2007 15:38:00 UTC

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