RE: NeuronDB RDF and OWL

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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Received on Wednesday, 14 March 2007 01:34:31 UTC