Cell ontology committee
Contribution toward a "structured naming convention"
This is motivated by the difficulty of a simple-minded user (my function) to navigate the current
neurolex cell ontology, based on common name, because of several problems: the common names follow
different formats; as a user I always look first to the region to find a cell; there is inconsistency in parentchild relations; the cell names do not provide unambiguous identification of each cell (I don't include the
multiple synonym question). To deal with these problems I've generated a complementary list, based on
region according to a "structured naming convention", according to some simple rules. The current list
under "Hierarchy: Cell" is in the left hand column; on the right is a complementary list of the same cells
according to a structured naming convention based on region (to make an unambiguous identifier for every
cell) with application of some simple rules for typographic consistency, etc. The rules are as follows:
Rule 1: sequence of terms:
First term is always main region
Next term is subregion (i.e. dorsal, ventral, neo, compacta, reticulata, main, accessory, etc.)
Next term is main cell type
Next term is cell subtype, and sub-subtype if necessary
This sequence of terms follows a strict parent child relationship; this keeps all the cells belonging
to the parent region together in the alphabetical listing, and all the cell subtypes under the same main type.
(For example, D multipolar cells and T multipolar cells are no longer at opposite ends of the list, but are
together under Cochlear nucleus (ventral) as multipolar D and multipolar T.)
This is probably the most controversial aspect of this format, because it makes some of the terms
initially unfamiliar. However, the advantages are that every cell has an unambiguous identity. Further, if
you know the region you can always find the cell type easily within it. Furthermore, the subtype term is
often an important discriminator (see, for example, Retina amacrine cell displaced and Retina amcrine cell
starburst); these discriminators between the two types of amacrine cells are at the last, where they are most
obvious, rather than at the start, which would have starburst, for example, as the parent of amacrine).
I haven't been sure whether terms should always end in cell or in a discriminator; open for
discussion.
Further minor editing aspects for consistency:
Rule 2: Only the first letter of the region is capitalized, plus any eponymous name. (the current list is
inconsistent in this respect)
Rule 3: Regions are given in noun form (as in subiculum pyramidal cell in current hierarchy) (the current
list is inconsistent in this respect)
Note that subheadings for cell types under one region are no longer necessary, because each cell
type already is identified with its region.
Please regard these rules as only suggestions to move the discussion along. I'm sure you'll see
cases where there could be a better way to formulate the terms.
The advantage of having both lists is that the user can use either the common name (left list) or the
region (right list) to find a particular cell. Also, using the right list, the user can determine if a particular
cell type is missing from a region and add it.
Left Row: current list
Right Row: Formatted by region and parent/child
cell name
[−] Neuron (114)
[×] 8th nerve ganglion cell (0)
[−] Amacrine cell (3)
[×] Displaced amacrine cell (0)
[×] Interplexiform amacrine cell (0)
Scarpa's ganglion cell (vestibular nerve)
Retina amacrine cell
Retina amacrine cell displaced
Retina interplexiform cell
[×] Starburst amacrine cell (0)
[×] Aspiny stellate cell (0)
[×] Basket cell (cortical) (0)
[×] Bipolar dendrite cell (0)
[−] Bushy cell (4)
[×] Globular Bushy Cell (0)
[×] Globular Bushy Cell (nifext 70) (0)
[×] Spherical Bushy Cell (0)
[×] Spherical Bushy Cell (nifext 71) (0)
[×] Cajal-Retzius Cell (0)
[×] Candelabrum cell (0)
[×] Cartwheel cell (0)
[×] Cerebellar Basket Cell (0)
[×] Cerebellar Golgi Cell (0)
[×] Cerebellar Stellate Cell (0)
[×] Cerebellar granule cell (0)
[×] Chandelier cell (0)
[×] Chandelier-type cell (0)
[×] Chemosensory receptor (0)
[×] Chestnut cell (0)
[×] Cholinergic Striatal Neuron (0)
Retina amacrine cell starburst
Retina stellate cell aspiny
Neocortex basket cell
Neocortex bipolar cell
Cochlear nucleus (ventral) bushy cell
Cochlear nucleus (ventral) globular bushy cell
ditto
Cochlear nucleus (ventral) spherical bushy cell
ditto
Neocortex Cajal-Retzius cell
Neocortex candelabrum cell
Cochlear nucleus (dorsal) cartwheel cell
Cerebellum basket cell
Cerebellum Golgi cell
Cerebellum stellate cell
Cerebellum granule cell
Neocortex chandelier cell
Neocortex chandelier-type cell
Chemosensory receptor cell
Neocortex chestnut cell
Neostriatum cholinergic cell; Neostriatum cholinergic
interneuron; Neostriatum giant cell of Kolliker
[×] Cholinergic nucleus basalis neuron (0) Basalis nucleus cholinergic neuron
[×] Ciliary Ganglion Neuron (0)
Ciliary ganglion neuron/cell
[×] Cortical Bipolar Cell (0)
Neocortex bipolar neuron
[−] Cortical Pyramidal cell (4)
Cortex (general) pyramidal cell/neuron
[+] Hippocampal pyramidal cell (3)
CA1, CA2, CA3, CA4 pyramidal cell/neuron
[×] Layer 2-3 pyramidal cell (0)
Neocortex pyramidal cell/neuron layer 2-3
[×] Layer 5-6 polymorphic cell (0)
Neocortex polymorphic cell/neuron layer 5-6
[×] Layer 5-6 pyramidal cell (0)
Neocortex pyramidal cell/neuron layer 5-6
[−] Cortical Stellate Cell (2)
Neocortex stellate cell
[×] Cortical Smooth Stellate Cell (0)
Neocortex stellate smooth cell
[×] Cortical Spiny Stellate Cell (0)
Neocortex stellate spiny cell
[×] D multipolar cell (0)
Cochlear nucleus (ventral) multipolar D cell
[×] DCN Gabaergic cell (0)
Cochlear nucleus (dorsal) gabaergic cell
[×] DCN glutamatergic cell (0)
Cochlear nucleus (dorsal) glutamatergic cell
[×] Deep interneuron (0)
Neocortex interneuron deep
[×] Dentate gyrus granule cell (0)
Dentate gyrus granule cell
[−] Dorsal root ganglion cell (nifext 84) (9) Dorsal root ganglion cell (shorten to DRG cell)
[×] Hair follicle cell (0)
DRG hair follicle cell
[×] IA ganglion cell (0)
DRG IA cell
[×] IB ganglion cell (0)
DRG IB cell
[×] II ganglion cell (0)
DRG II cell
[×] Meissner's corpuscle cell (0)
DRG Meissner's corpuscle cell
[×] Merckel disc cell (0)
DRG Merckel disc cell
[×] Pacinian corpuscle cell (0)
DRG Pacinian corpuscle cell
[×] Pain cell (0)
DRG pain cell
[×] Temperature cell (0)
DRG temperature cell
[×] Dorsal spinocerebellar tract cell (0)
Spinocerebellar (dorsal) tract cell
[×] Dorsal swim interneuron (0)
Leech swim (dorsal) interneuron (?)
[×] Double Bouquet Cell (0)
Neocortex bouquet double cell
[×] Fibroblast (0)
[×] Flexor reflex afferent interneuron (0)
Spinal cord ventral horn interneuron FRA
[×] Gaba/parvalbumin interneuron (0)
Striatum (neo) GABA/Parvalbumin interneuron
[×] Giant cell (0)
Cochlear nucleus (dorsal) giant cell
[×] Globus pallidus intrinsic cell (0)
Globus pallidus intrinsic cell
[×] Globus pallidus principle cell (0)
Globus pallidus principal cell
[×] Glomerular layer cell (0)
Olfactory bulb glomerular layer cell
[×] Golgi II cell (0)
Which region(s)?
[×] Golgi cell (0)
Which region(s)?
[×] Gracilis Nucleus intrinsic cell (0)
Gracilis nucleus intrinsic cell
[×] Gracilis Nucleus principal cell (0)
Gracilis nucleus principal cell
[×] Granule Cell DCN (0)
Cochlear (dorsal) nucleus granule cell
[+] Hair cell (2)
Hair cell (which region?)
[−] Cochlear Hair Cell (2)
Cochlea hair cell
[×] Cochlear Inner Hair Cell (0)
Cochlea hair cell inner
[×] Cochlear Outer Hair Cell (0)
Cochlea hair cell outer
[×] Vestibular Hair Cell (0)
Vestibular hair cell
[−] Hair cell (nifext 61) (4)
Hair cell
[×] Hair cell Type 1 (0)
Hair cell type I (also Hair cell type II)
[×] Hair cell macula (0)
Macula hair cell
[×] Inner Hair Cell (0)
Hair cell inner
[×] Outer Hair Cell (0)
Hair cell outer
[×] Hippocampal basket cell (many types) (0)
[×] Horizontal cell (olfactory) (0)
Olfactory cortex horizontal cell
[×] Horizontal cell (retina) (0)
Retina horizontal cell
[×] IA interneuron (0)
Spinal cord ventral horn interneuron IA
[×] IB interneuron (0)
Spinal cord ventral horn interneuron IB
[×] II interneuron (0)
Spinal cord ventral horn interneuron II
[×] Inferior colliculus intrinsic cell (0)
Colliculus inferior intrinsic cell/neuron
[×] Inferior colliculus principal cell (0)
Colliculus inferior principal cell/neuron
[×] Islets of Calleja Gaba interneuron (0)
Olfactory tubercle Islets of Calleja GABA cell/interneuron
[×] Islets of Calleja dopamine cell (0)
Olfactory tubercle Islets of Calleja DA cell/neuron
[×] Large interneuron thalamic (0)
Thalamus interneuron large
[×] Locus coeruleus noradrenergic neuron (0) Locus coeruleus NA neuron
[×] Lugaro cell (0)
Cerebellum Lugaro cell
[×] M-cone cell (0)
Retina Cone M
[×] Martinotti cell (0)
Neocortex Martinotti cell
[×] Medium Spiny Cell (0)
Neostriatum spiny medium cell/neuron
[×] Medium ganglion cell (0)
?
[×] Medium spiny cell (0)
Same as above: Neostriatum spiny medium cell/neuron
[×] Metacerebral cell (0)
Aplysia cerebral ganglion metacerebral cell
[×] Mitral cell (0)
Olfactory bulb (main or accessory) mitral cell
[×] Mossy cell (0)
?
[−] Motor neuron (4)
also: Motoneurone, motoneuron
[×] Alpha Motor Neuron (0)
Spinal cord ventral horn motor neuron alpha
[+] Autonomic motor neuron (1)
Spinal cord ventral horn motor neuron autonomic
[×] Sympathetic motor neuron (0)
Spinal cord intermediate horn motor neuron sympathetic
[×] Beta motor neuron (0)
Spinal cord ventral horn motor neuron beta
[×] Gamma Motor Neuron (0)
Spinal cord ventral horn motor neuron gamma
[×] Multipolar cell of VCN (0)
Cochlear (ventral) nucleus multipolar cell
[×] Neurogliaform cell (0)
CA1 neurogliaform cell
[×] Nucleus of the Solitary Tract intrinsic cell (0) Solitary tract nucleus intrinsic cell/neuron
[×] Nucleus of the Solitary Tract principal cell (0) Solitary tract nucleus principal cell/neuron
[×] Octopus Cell (0)
Cochlear (ventral) nucleus octopus cell
[×] Olfactory Granule cell (0)
Olfactory bulb (main/accessory) granule cell
[×] Olfactory receptor neuron (0)
Olfactory receptor cell; olfactory sensory neuron/cell
[×] Pars reticulata Gaba interneuron (0)
Substania nigra pars reticulata interneuorn GABA
[×] Pars reticulata principal neuron (0)
Substantia nigra pars reticulata principal cell/neuron
[−] Photoreceptor Cell (1)
Retina photoreceptor cell
[+] Eye Photoreceptor Cell (2)
Retina cone S (also M, L)
Retina rod
[×] Polymorphic cell (0)
Piriform (olfactory) cortex polymorphic cell
[×] Principal Cells Medial Nucleus Trapezoid Body (0) Trapezoid body medial nucleus principal
cell/neuron
[×] Principal neuron of medial trapezoid body (0) ditto
[×] Proprioception intersegmental cell (0) Spinal cord ventral horn intersegmental cell proprioception
[×] Purkinje Cell (0)
Cerebellum Purkinje cell (not cardiac Purkinje cell)
[−] Pyramidal Cell (6)
Pyramidal cell/neuron
[−] Cortical Pyramidal Neuron (3)
Neocortex pyramidal cell/neuron
[×] Layer 2 3 Pyramidal neuron
Neocortex pyramidal cell/neuron layer 2/3
[×] Layer 3 Pyramidal neuron
Neocortex pyramidal cell/neuron layer 3
[×] Layer 5 Pyramidal neuron
Neocortex pyramidal cell/neuron layer 5
[−] Hippocampal Pyramidal Neuron (2)
Hippocampus (CA) pyramidal cell/neuron
[×] Hippocampal CA1 Pyramidal Neuron (0) Hippocampus CA1 pyramidal cell/neuron
(also CA2, CA4)
[×] Hippocampal CA3 Pyramidal Neuron (0) Hippocampus CA3 pyramidal cell/neuron
[×] Pyramidal cell DCN (0)
Cochlear (dorsal) nucleus pyramidal neuron; also called
Cochlear (dorsal) nucleus fusiform cell
[×] Pyramidal cell basolateral amygdalar nucleus (0) Amygdala basolateral nucleus pyramidal
cell/neuron
[×] Pyramidal cell corticomedial amygdalar nucleus (0) Amygdala corticomedial nucleus pyramidal
cell/neuron
[×] Subiculum pyramidal cell (0)
Subiculum pyramidal cell/neuron
[×] Renshaw cell (0)
Spinal cord ventral horn interneuron Renshaw
[−] Retinal Bipolar cell (4)
Retina bipolar cell
[×] Midget cell (0)
Retina bipolar cell midget
[×] Off cell (0)
Retina bipolar cell off
[×] On cell (0)
Retina bipolar cell on
[×] Parasol cell (0)
Retina bipolar cell parasol
[−] Retinal Ganglion Cell (5)
Retina ganglion cell
[×] Large field ganglion cell (0)
Retina ganglion cell large field
[×] Medium complex ganglion cell (0
Retina ganglion cell medium complex
[×] Medium simple ganglion cell (0)
Retina ganglion cell medium simple
[×] Small complex ganglion cell (0)
Retina ganglion cell small complex
[×] Small simple ganglion cell (0)
Retina ganglion cell small simple
[×] SOM cell (0)
Neostriatum SOM cell/interneuron
[×] SOM/NOS interneuron (0)
Neostriatum SOM/NOS cell/interneuron
[×] Short axon cell (0)
many regions
[×] Small interneuron thalamic (0)
Thalamus interneuron small
[×] Small pyramidal neuron (0)
Pyramidal cell/neuron (Olfactory cortex; Neocortex)
[×] Spindle neuron (0)
?
[×] Spiny bipolar cell (0)
?
[×] Spiny stellate cell (0)
see neostriatum, neocortex layer 4
[×] Stellate cell cortical (0)
Neocortex stellate cell
[+] Substantia nigra dopaminergic cell (0) Substantia nigra pars compacta dopaminergic cell
[×] Superficial interneuron (0)
?
[×] Supporting cell (0)
Main olfactory epithelium supporting (sustentacular) cell
[×] T multipolar cell (0)
Cochlear (ventral) nucleus multipolar T cell
[×] Taste Bud Type 1 cell (0)
Taste bud type 1 cell
[×] Taste Bud Type 2 cell (0)
Taste bud type 2 cell
[+] Thalamic relay cell (1)
Thalamus relay cell/neuron; also Thalamocortical cell/neuron
[×] Thalamic reticular neuron (0)
Thalamic reticular nucleus cell/neuron
[×] Trapezoid body intrinsic cell (0)
Trapezoid body intrinsic cell/neuron
[×] Trapezoid body principal cell (0)
Trapezoid body principal cell/neuron
[×] Trigeminal Nucleus intrinsic cell (0)
Trigeminal nucleus intrinsic cell/neuron
[×] Trigeminal Nucleus principle cell (0)
Trigeminal nucleus principal cell
[×] Tufted cell (0)
Olfactory bulb (main and accessory) tufted cell
[×] Unipolar brush cell (0)
[×] Vertical Cell (0)
[×] Vestibular ganglion cell (0)
Cerebellum unipolar brush cell
Cochlear (dorsal) nucleus vertical cell
Vestibular ganglion cell
One of the next steps must be to add invertebrate cells!