[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
