Re: NeuronDB RDF and OWL

That would be wonderful, Luis.

Cheers,
Bill

On Mar 13, 2007, at 6:34 PM, Luis Marenco wrote:

>
>
> I'll annotate semantically all the EAV/CR elements in SenseLab.  
> This way the
> next time the OWL convertion routine will be describe the  
> relationships more
> accurately.
>
> e.g.:
> http://senselab.med.yale.edu/senselab/site/dbMeta/ 
> eavMD_Attributes.asp?at=71
>
> ________________________
> Luis Marenco
> Yale Center for Medical Informatics
>
>
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of
> samwald@gmx.at
> Sent: Tuesday, March 13, 2007 8:48 AM
> To: Kei Cheung; public-semweb-lifesci@w3.org
> Subject: Re: NeuronDB RDF and OWL
>
>
>
>> We just finished exporting the NeuronDB of Senselab into RDF and OWL.
>>
>> http://neuroweb.med.yale.edu/senselab/
>
>
> Great!
>
> Here are some thoughts I had while browsing through the OWL
> version (I post them in public so others do not give you
> redundant feedback):
>
> According to the Pellet reasoner, the ontology is fully consistent.
>
> I guess you plan to change this in the final release anyways,
> but all the classes need to have a value for the rdfs:label
> property. The URIs are not intended to be read by humans, so
> none of the classes has an actual name in the current version
> of the ontology.
>
> Assuming that the class names will be identical with the current URIs:
>
> "Forebrain" should be renamed to "Prosencephalon", to be
> consistent with the naming of the other major brain regions
> (e.g. "mesencephalon", "metencephalon"). Of course, you could
> also rename the other classes to the English trivial names
> ("midbrain" etc.).
>
> With the current names of the classes, many of the
> class-subclass relations are in fact whole-part relations (e.g.
> the ontology states that "Vestibular_Organ" is a subclass of
> "Cochlea", but in fact it is a part of the cochlea). If you
> want to preserve the current class structure, but be
> ontologically consistent, I would suggest to rename such
> classes from "X" to "X or part of X". For example,
> "Vestibular_Organ" would become
> "Vestibular_Organ_or_part_of_Vestibular_Organ". Now it would be
> correct to state that "Cochlea" is a subclass of
> "Vestibular_Organ_or_part_of_Vestibular_Organ", because the
> superclass includes parts.
>
> The IDs/names of the subclasses of "Dendritic Compartment" and
> "Axon" could be a little clearer (I assume that d, m and p
> stand for distal, medial and proximal, AH is axon hillock and T
> is terminal?).
>
> Some of the subclasses of "Neuron_Receptor" and
> "Neuron_Transmitter" (Neurotransmitter) have names in the
> plural form (e.g. "Ion_Receptors"). This should be changed to
> singular to be consistent with the rest of the ontology.
>
> Using Protege 3.2, I have troubles view the annotations that
> relate facts to individuals belonging to the "Notes" class.
> Looking at the source, I see that rdfs:seeAlso and blank nodes
> were used. I guess it is Protege's fault that these relations
> are not displayed.
>
>
> cheers,
> Matthias Samwald
>
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>

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