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Re: Martone's Ontology

From: William Bug <William.Bug@DrexelMed.edu>
Date: Thu, 11 Jan 2007 12:20:24 -0500
Message-Id: <480AC778-A451-4A64-8099-41FDE63EAA2F@DrexelMed.edu>
Cc: "'public-semweb-lifesci'" <public-semweb-lifesci@w3.org>
To: Donald Doherty <donald.doherty@brainstage.com>
Hi Don,

I think it is ready for use.

Here is a presentation Maryann gave recently on use of SAO to  
annotate electron tomographic data sets:
	
Do you have a copy of their SfN presentation?

Maryann or her grad student Stephen Larson who is working directly on  
SAO development would be able to provide the definitive answer to  
your request.

As to your statement regarding its use, I completely agree.  It would  
also be useful to speak with Stephen to find out whether they have  
talked with the GO developers regarding alignment with the GO- 
CellularComponent subsumptive trunk, which I believe is being  
refactored to bring it more in line with OBO Foundry recommendations.  
There are also other ontologies and classification schemes covering  
macromolecular complexes.  Stephen may have some suggestions on how  
to integrate those, as well.

Finally, I believe Stephen may have valuable suggestions regarding  
the use of Rule-based formalisms to represent the more complex  
subcellular component relations.

Cheers,
Bill
	
On Jan 11, 2007, at 10:42 AM, Donald Doherty wrote:

> 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
>
>
>
>
>
>
>
>

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 17:20:35 UTC

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