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RE: NeuronDB RDF and OWL

From: Kashyap, Vipul <VKASHYAP1@PARTNERS.ORG>
Date: Wed, 14 Mar 2007 16:44:50 -0400
Message-ID: <2BF18EC866AF0448816CDB62ADF653810660E96D@PHSXMB11.partners.org>
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>
Cc: "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>
Alan,

You have proposed some modeling suggestions and of course alignment with the OBO
relations ontology.

Other than expressing the semantics of these classes precisely, it will be great
if you and someone in this group could identify the potential impact
of these modeling choices on:
- Enabling different types of integration that were not feasible before
- Enabling different types of inferences which would enable further integration
not possible before.

Alternatively, for the purpose of the demo, one could just do a shallow
alignment so that different data sets can be integrated.

Any thoughts?

---Vipul

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-lifesci-
> request@w3.org] On Behalf Of Alan Ruttenberg
> Sent: Wednesday, March 14, 2007 12:38 AM
> To: public-semweb-lifesci hcls
> Subject: Re: NeuronDB RDF and OWL
> 
> 
> [sent earlier directly to Kei, but we though it might be of general
> interest]
> 
> Some comments on the NeuronDB modeling:
> 
> If there are textual definitions associated with the classes, it
> would be helpful to include them as rdf:comments. If not, consider
> going to
> some reference and choosing definitions that capture your intent.
> 
> Type of relationship among parts:
> 
> Consider (indentation = subclassof)
>   !neurondb:BrainRegion
>      !neurondb:ForeBrain
>        !neurondb:Neocortex
>           !neurondb:Visual_Motor
> 
> Every forebrain is a BrainRegion (isa)
> Every Neocortex is part of a ForeBrain (part_of)
> Every Visual Motor region of the Neocortex is a part_of a Neorcortex
> (part_of, naming)
> 
> In other cases my lack of anatomy doesn't let me know which relation
> is intended.
> Is the retina a part of the diencephalon or is it connected to the
> diencephalon
> 
> archicortex (ar·chi·cor·tex) (ahr”kĭ-kor´teks)   [TA] that
> portion of the cerebral cortex that, with the paleocortex, develops
> in association with the olfactory system, and which is
> phylogenetically older than the neocortex and lacks its layered
> structure. The embryonic archicortex corresponds to the cortex of the
> dentate gyrus and hippocampus in mature mammals. Called also
> archaeocortex or archeocortex, archipallium, and olfactory cortex.
> 
> So is the hippocampus part of the archicortex, or does it derive_from
> the archicortex?
> 
> Similarly the brain compartments. Dendrite is a compartment,
> basal_dendrite_compartment is part_of Dendrite. If all dendrites have
> basal_dendrite_compartment consider also including the has_part
> relationship.
> 
> belongToBrainRegion: consider using ro:located_in or ro:part_of
> (http://obofoundry.org/ro/)
> 
> Singular/Plural: Neuron_Receptor  vs.  Peptide_Receptors
> Consider keeping everything in the singular.
> 
> Gaba is as neuron_receptor and a neuron_transmitter. Is Gaba a
> neurotransmitter, or a receptor? Distinguish the receptor from the
> thing received.
> 
> The note instances don't seem to be attached to anything currently.
> Consider not creating the anonymous instance and merging their
> contents into the rdfs:comment of the thing that has the note.
> 
> Disjoints - consider adding disjoints at each level, where appropriate.
> 
> Ok, that's enough for now. Let me know if you want to TC to discuss
> these in more detail. You can forward this to the list if you are
> comfortable - I didn't want to unless you do.
> 
> -Alan
> 
> On Mar 12, 2007, at 5:02 PM, Kei Cheung wrote:
> 
> >
> > Hi,
> >
> > We just finished exporting the NeuronDB of Senselab into RDF and OWL.
> >
> > http://neuroweb.med.yale.edu/senselab/

> >
> > Best,
> >
> > -Kei
> >
> >
> >
> 






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Received on Wednesday, 14 March 2007 20:45:05 UTC

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