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: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of
[EMAIL PROTECTED]
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
--
"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt GMX TopMail testen: www.gmx.net/de/go/mailfooter/topmail-out
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 - [EMAIL PROTECTED]
