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RE: Mapping NeuronDB to MeSH to BAMS

From: Donald Doherty <donald.doherty@brainstage.com>
Date: Tue, 20 Mar 2007 15:13:20 -0400
To: "'Kei Cheung'" <kei.cheung@yale.edu>
Cc: <public-semweb-lifesci@w3.org>
Message-ID: <000e01c76b23$d4283260$2f01a8c0@Brainstage>

Thank you Kei...it's a pleasure working on this with you and the rest of the

You point out mapping the specific to the general (i.e., "CA3 pyramidal
neuron" to "pyramidal cell"). Another big mapping challenge is going from
the general to the specific. If an ontology like BAMS only lists detailed
terms, we need to map the more general term to a collection of specific
terms (i.e., Amygdala to the many parts of the Amygdala stated in BAMS).

Best wishes,

-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of Kei Cheung
Sent: Tuesday, March 20, 2007 9:58 AM
To: donald.doherty@brainstage.com
Cc: public-semweb-lifesci@w3.org
Subject: Re: Mapping NeuronDB to MeSH to BAMS

Hi Don,

Thanks a lot for your effort in establishing mappings between Senselab 
brain regions/cell names and BAMS brain brain regions/cell names. Such 
mappings are not a trivial task as they require a significant amount of 
domain knowledge (even neursocientists sometimes have difficult times in 
mapping terms between different data sources). While some of the 
mappings are one-to-one, others are one-to-many (e.g., CA1 pyramidal 
neuron and CA3 pyramidal neuron in SenseLab are mapped to Pyramidal 
Cells in MeSH). From the semantic web perspective, I think it would be 
interesting to see how to use things like OWL constructs to establish 
such mappings (both one-to-one and one-to-many) to facilitate data 



Donald Doherty wrote:
> I've mapped all of the NeuronDB terms on 
> http://senselab.med.yale.edu/senselab/NeuronDB/ndbRegions.asp?sr=1 to 
> MeSH and BAMS as best I could (see attached spreadsheet).
> The BAMS Cell Names, at least those provided, are only useful within a 
> sharply defined domain and level of detail. We need something better 
> for mapping at the cell level. MeSH doesn't provide good cell level 
> mapping either.
> Don
> -----
> Donald Doherty, Ph.D.
> Brainstage Research, Inc.
> www.brainstage.com <http://www.brainstage.com/>
> donald.doherty@brainstage.com <mailto:donald.doherty@brainstage.com>
> 412-683-1410
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Received on Tuesday, 20 March 2007 19:08:50 UTC

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