cell types, brain regions mentioned in gensat

I'm making progress in converting gensat to rdf.

For mapping considerations, here is the list of cell types mentioned  
in gensat, followed by the list of brain regions. If we are going to  
do cross queries we will need to find standard names for these. Bill,  
are these classes in birnlex? If not, we need to spawn a task to  
identify a vocabulary we will use for these.

Note that we get a region<->neuron association via gensat where they  
annotation both a region and a cell type.
Note also some amusements, like the presence of lung as region in an  
ostensibly CNS database.

I've also attached the "ontology.csv" from the Allen Brain Explorer  
application, which I presume gives their hierarchy of brain regions/ 
subregions. I've put labels on the first 3 columns which I think  
encode the hierarchy.

The other interesting annotations, are the gene, the location,  
orientation, and size of the image, as well as some broad categories  
of qualitative expression, such as whether it is localized of widely  
expressed. There is also gender and a few categories of age.

There are ~60K images in gensat.

BTW, if someone has a theory of what the other number in ontology.xls  
are, I'm all ears.

-Alan

CellType(Cell subtype)
------------------------------
ependymal cell
glial cell
glial cell(Bergmann glia)
glial cell(CA1 pyramidal cell)
glial cell(Purkinje cell)
glial cell(astrocyte)
glial cell(fibers)
glial cell(granule cell of MOB)
glial cell(granule cell)
glial cell(interneuron)
glial cell(olfactory ensheathing cell)
glial cell(oligodendrocyte)
glial cell(other)
glial cell(periglomerular cell of MOB)
glial cell(processes)
neuron
neuron(Bergmann glia)
neuron(CA1 pyramidal cell)
neuron(CA2 pyramidal cell)
neuron(CA3 pyramidal cell)
neuron(Purkinje cell)
neuron(basket cell)
neuron(dentate hilar cell)
neuron(fibers)
neuron(granule cell of AOB)
neuron(granule cell of MOB)
neuron(granule cell)
neuron(interneuron)
neuron(mitral cell of AOB)
neuron(mitral cell of MOB)
neuron(motor neuron)
neuron(not clear)
neuron(other)
neuron(periglomerular cell of AOB)
neuron(periglomerular cell of MOB)
neuron(processes)
neuron(pyramidal cell)
neuron(sensory neuron/ primary)
neuron(striatal matrix neuron)
neuron(striatal patch neuron)
not clear
not clear(fibers)
not clear(processes)
other
vascular cell
vascular cell(fibers)
vascular cell(processes)


Region
----------------
Accessory olfactory bulb
Accumbens nucleus
Amygdala
Anterior Olfactory Nucleus
Anterior commissure
Basal Forebrain
Cartilage
Caudate Putamen
Cerebellum
Cerebral cortex
Cerebral peduncle
Clark nucleus
Claustrum
Corpus callosum
Diencephalon
Dorsal Horn
Dorsal funiculus
Dorsal root ganglia
Entorhinal Cortex
External capsule
Fasciculus retroflexus
Fornix
Gastrointestinal tract
Globus Pallidus
Glossopharyngeal ganglion
Hippocampus
Hypothalamus
Inferior cerebellar peduncle
Inferior olive
Intermediolateral cell column
Internal capsule
Islands of Calleja
Lamina 10
Lateral funiculus
Lateral lemniscus
Lateral olfactory tract
Leptomeninges
Lung
Median septum
Medulla
Meninges
Mesencephalon
Midbrain
Middle cerebellar peduncle
Muscle
Nigrostriatal bundle
Olfactory Bulb
Olfactory epithelium
Olfactory tubercle
Optic tract
Piriform cortex
Pituitary gland
Pons
Pons+Medulla
Pretectal nucleus
Pyramidal tract
Rhombencephalon
Rostral migratory stream
Septum
Spinal trigeminal tract
Stria medullaris thalami
Stria terminalis
Subcommissural organ
Subicular cortex
Substantia Nigra
Subventricular zone
Telencephalon
Thalamus
Trigeminal ganglion
Trigeminal nerve
Ventral Horn
Ventral funiculus
Ventral pallidum
Ventral striatum
Ventral tegmental area
Vomeronasal organ
retina
ventricular zone