NIF Phenotypes
type: Ontology
imports: phenotype-core.ttl
comment: A taxonomy of phenotypes used to model biological types as collections of measurements.

Accommodating spiking phenotype
type: Class
subclass of: Spiking phenotype
disjoint with: Non accommodating spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Accommodating spiking

Autonomic nervous system population phenotype
type: Class
subclass of: Cell phenotype
comment: used to account for populations that are part of distinct autonomic nervous system subdivisions
hidden label: Autonomic nervous system population

Anterior projecting
type: Class
subclass of: Projection phenotype
comment: projects in the anterior direction of the housing structure
use object property: hasProjectionPhenotype
hidden label: Anterior projecting

Apical dendrite phenotype
type: Class
subclass of: Dendrite phenotype
comment: When used directly indicates the presence or absense of an apical dendrite. Rather than subclassing directly, could be combined with general dendrite phenotypes to allow specificity.
use object property: hasDendriteMorphologicalPhenotype
hidden label: Apical dendrite

Axon morphological phenotype
type: Class
subclass of: Axon phenotype

Axon phenotype
type: Class
subclass of: Phenotype
use object property: hasAxonPhenotype

Basket phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Bipolar phenotype
disjoint with: Bistratified phenotype
disjoint with: Bitufted phenotype
disjoint with: Chandelier phenotype
disjoint with: Cone phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Basket

Biopolar pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Horizontal pyramidal phenotype
disjoint with: Inverted pyramidal phenotype
disjoint with: Narrow pyramidal phenotype
disjoint with: Small pyramidal phenotype
disjoint with: Star pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Biopolar pyramidal

Bipolar phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Bistratified phenotype
disjoint with: Bitufted phenotype
disjoint with: Chandelier phenotype
disjoint with: Cone phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Bipolar

Bistratified phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Bitufted phenotype
disjoint with: Chandelier phenotype
disjoint with: Cone phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Bistratified

Bitufted phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Chandelier phenotype
disjoint with: Cone phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Bitufted

Branching phenotype
type: Class
subclass of: Dendrite phenotype
use object property: hasDendriteMorphologicalPhenotype
hidden label: Branching

Cell phenotype
type: Class
subclass of: Phenotype

Chandelier phenotype
type: Class
synonym: AxoAxonicPhenotype
subclass of: Morphological phenotype
disjoint with: Cone phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Chandelier

Cone phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Disc phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Cone

Cortico fugal
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Cortico fugal

Cortico pontine
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Cortico pontine

Cortico spinal
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Cortico spinal

Cortico striatal
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Cortico striatal

Cortico thalamic
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Cortico thalamic

Dendrite morphological phenotype
type: Class
subclass of: Dendrite phenotype

Dendrite phenotype
type: Class
subclass of: Phenotype
use object property: hasDendriteMorphologicalPhenotype

Dense axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Dense axon

Descending axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Descending axon

Direct pathway
type: Class
comment: Needs work
hidden label: Direct pathway

Disc phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Double bouquet phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Disc

Dopaminergic phenotype
type: Class
subclass of: Expression phenotype
comment: figure out how to regularize these since I have used ilxtr:parvalbumin elsewhere, probably ilxtr:phenotype/thing will be best
use object property: hasExpressionPhenotype
hidden label: Dopaminergic

Double bouquet phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Granule phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Double bouquet

Early bifurcating phenotype
type: Class
subclass of: Branching phenotype
disjoint with: Late bifurcating phenotype
use object property: hasDendriteMorphologicalPhenotype
hidden label: Early bifurcating

Early bifurcating thick tufted pyramidal phenotype
type: Class
subclass of: Thick tufted pyramidal phenotype
disjoint with: Late bifurcating thick tufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Early bifurcating thick tufted pyramidal

Early bifurcating tufted pyramidal phenotype
type: Class
subclass of: Tufted pyramidal phenotype
disjoint with: Late bifurcating tufted pyramidal phenotype
disjoint with: Narrow tufted pyramidal phenotype
disjoint with: Slender tufted pyramidal phenotype
disjoint with: Thick tufted pyramidal phenotype
comment: we are not modelling dendrite phenotypes directly at the moment so we cant break about EB/LB
use object property: hasMorphologicalPhenotype
hidden label: Early bifurcating tufted pyramidal

Electrophysiological phenotype
type: Class
subclass of: Cell phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Electrophysiological

Enteric phenotype
type: Class
subclass of: Cell phenotype
hidden label: Enteric

Expression phenotype
type: Class
synonym: molecular phenotype
subclass of: Cell phenotype
use object property: hasExpressionPhenotype
hidden label: Expression

Fast spiking phenotype
type: Class
subclass of: Spiking phenotype
disjoint with: Regular spiking non pyramidal phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Fast spiking

Granule phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Ivy phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Granule

Horizontal axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Horizontal axon

Horizontal pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Inverted pyramidal phenotype
disjoint with: Narrow pyramidal phenotype
disjoint with: Small pyramidal phenotype
disjoint with: Star pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Horizontal pyramidal

Interneuron phenotype
type: Class
subclass of: Intrinsic phenotype
comment: this is the 'general' morphological phenotype that might be made up of soma/axon/dendrite
hidden label: Interneuron

Intestino fugal projection phenotype
type: Class
subclass of: Projection phenotype
comment: projects out of the intestines
use object property: hasProjectionPhenotype
hidden label: Intestino fugal projection

Intrinsic phenotype
type: Class
subclass of: Axon phenotype
comment: local projections only? (define local) equivalent to LocalAxonOnly, is this an axon phenotype or an axon location phenotype?
hidden label: Intrinsic

Inverted pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Narrow pyramidal phenotype
disjoint with: Small pyramidal phenotype
disjoint with: Star pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Inverted pyramidal

Ivy phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Martinotti phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Ivy

Large axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Large axon

Large basket phenotype
type: Class
subclass of: Basket phenotype
disjoint with: Nest basket phenotype
disjoint with: Small basket phenotype
use object property: hasMorphologicalPhenotype
hidden label: Large basket

Late bifurcating phenotype
type: Class
subclass of: Branching phenotype
use object property: hasDendriteMorphologicalPhenotype
hidden label: Late bifurcating

Late bifurcating thick tufted pyramidal phenotype
type: Class
subclass of: Thick tufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Late bifurcating thick tufted pyramidal

Late bifurcating tufted pyramidal phenotype
type: Class
subclass of: Tufted pyramidal phenotype
disjoint with: Narrow tufted pyramidal phenotype
disjoint with: Slender tufted pyramidal phenotype
disjoint with: Thick tufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Late bifurcating tufted pyramidal

Local axon
type: Class
subclass of: Axon phenotype
hidden label: Local axon

Local axon only
type: Class
subclass of: Axon phenotype
comment: model this as NegPhenotype(ilxtr:RemoteAxon)? This really feels like we are overcomplicating things… all we should need to know is that in projects to its own brain region… or better to a specific cell population that has a known location
hidden label: Local axon only

Martinotti phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Medium spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Martinotti

Medium spiny phenotype
type: Class
subclass of: Morphological phenotype
subclass of: Spiny phenotype
disjoint with: Neurogliaform phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
comment: we really should be able to deal with spines in a convenient way
use object property: hasMorphologicalPhenotype
hidden label: Medium spiny

Morphological phenotype
type: Class
subclass of: Cell phenotype
comment: this is the 'general' morphological phenotype that might be made up of soma/axon/dendrite
use object property: hasMorphologicalPhenotype
hidden label: Morphological

Motor phenotype
type: Class
subclass of: Projection phenotype
comment: motor neuron phenotype, motor projecting phenotype, muscle projecting phenotype, hasForwardConnectionPhenotype some myocyte, implies
hidden label: Motor

Narrow phenotype
type: Class
subclass of: Trunk phenotype
disjoint with: Slender phenotype
disjoint with: Thick phenotype
comment: I get the feeling that this is actually a synonym for slender, ma2015sup uses 'thin' but that has nasty collsions with 'thick' for short naming (sigh)
use object property: hasDendriteMorphologicalPhenotype
hidden label: Narrow

Narrow pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Small pyramidal phenotype
disjoint with: Star pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
comment: this class is circumspect, and may actually be NarrowTuftedPyramidalPhenotype
use object property: hasMorphologicalPhenotype
hidden label: Narrow pyramidal

Narrow tufted pyramidal phenotype
type: Class
subclass of: Tufted pyramidal phenotype
disjoint with: Slender tufted pyramidal phenotype
disjoint with: Thick tufted pyramidal phenotype
comment: issues with NarowPyramidalPhenotype
use object property: hasMorphologicalPhenotype
hidden label: Narrow tufted pyramidal

Nest basket phenotype
type: Class
subclass of: Basket phenotype
disjoint with: Small basket phenotype
use object property: hasMorphologicalPhenotype
hidden label: Nest basket

Neurogliaform dense axon phenotype
type: Class
subclass of: Neurogliaform phenotype
use object property: hasMorphologicalPhenotype
hidden label: Neurogliaform dense axon

Neurogliaform phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Pyramidal phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Neurogliaform

Neurogliaform sparse axon phenotype
type: Class
subclass of: Neurogliaform phenotype
use object property: hasMorphologicalPhenotype
hidden label: Neurogliaform sparse axon

Parasympathetic Post-Ganglionic phenotype
type: Class
subclass of: Parasympathetic phenotype
subclass of: Post ganglionic phenotype
hidden label: Parasympathetic Post-Ganglionic

Parasympathetic Pre-Ganglionic phenotype
type: Class
subclass of: Parasympathetic phenotype
subclass of: Pre ganglionic phenotype
hidden label: Parasympathetic Pre-Ganglionic

Sympathetic Post-Ganglionic phenotype
type: Class
subclass of: Post ganglionic phenotype
subclass of: Sympathetic phenotype
hidden label: Sympathetic Post-Ganglionic

Sympathetic Pre-Ganglionic phenotype
type: Class
subclass of: Pre ganglionic phenotype
subclass of: Sympathetic phenotype
hidden label: Sympathetic Pre-Ganglionic

Non accommodating spiking phenotype
type: Class
subclass of: Spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Non accommodating spiking

Parasympathetic phenotype
type: Class
subclass of: Autonomic nervous system population phenotype
disjoint with: Sympathetic phenotype
hidden label: Parasympathetic

Perforant pathway associated
type: Class
comment: Needs work
hidden label: Perforant pathway associated

Petilla initial burst spiking phenotype
type: Class
synonym: petilla b
subclass of: Petilla initial spiking phenotype
disjoint with: Petilla initial classical spiking phenotype
disjoint with: Petilla initial delayed spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla initial burst spiking

Petilla initial classical spiking phenotype
type: Class
synonym: petilla c
subclass of: Petilla initial spiking phenotype
disjoint with: Petilla initial delayed spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla initial classical spiking

Petilla initial delayed spiking phenotype
type: Class
synonym: petilla d
subclass of: Petilla initial spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla initial delayed spiking

Petilla initial spiking phenotype
type: Class
subclass of: Spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla initial spiking

Petilla sustained accommodating phenotype
type: Class
synonym: petilla ac
subclass of: Petilla sustained spiking phenotype
disjoint with: Petilla sustained irregular phenotype
disjoint with: Petilla sustained non accommodating phenotype
disjoint with: Petilla sustained stuttering phenotype
comment: how do we deal with the fact that there are other accommodating phenotypes‚ multiple parent is annoying
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla sustained accommodating

Petilla sustained irregular phenotype
type: Class
synonym: petilla ir
subclass of: Petilla sustained spiking phenotype
disjoint with: Petilla sustained non accommodating phenotype
disjoint with: Petilla sustained stuttering phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla sustained irregular

Petilla sustained non accommodating phenotype
type: Class
synonym: petilla nac
subclass of: Petilla sustained spiking phenotype
disjoint with: Petilla sustained stuttering phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla sustained non accommodating

Petilla sustained spiking phenotype
type: Class
subclass of: Spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla sustained spiking

Petilla sustained stuttering phenotype
type: Class
synonym: petilla stut
subclass of: Petilla sustained spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Petilla sustained stuttering

Posterior projecting
type: Class
subclass of: Projection phenotype
comment: projects in the posterior direction of the housing structure
use object property: hasProjectionPhenotype
hidden label: Posterior projecting

Post ganglionic phenotype
type: Class
subclass of: Autonomic nervous system population phenotype
disjoint with: Pre ganglionic phenotype
hidden label: Post ganglionic

Pre ganglionic phenotype
type: Class
subclass of: Autonomic nervous system population phenotype
hidden label: Pre ganglionic

Projection phenotype
type: Class
subclass of: Axon phenotype
comment: we don’t always have target location information, sometimes the best we get is ‘the axon leaves the section’, equivalent to RemoteAxon
hidden label: Projection

Pyramidal phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Rod phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Pyramidal

Regular spiking non pyramidal phenotype
type: Class
subclass of: Spiking phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Regular spiking non pyramidal

Remote axon
type: Class
subclass of: Axon phenotype
comment: hasProjectionPhenotype (some (class brainRegion (not (brainRegion containing this neruon))))
hidden label: Remote axon

Remote axon only
type: Class
subclass of: Axon phenotype
comment: model this as NegPhenotype(ilxtr:LocalAxon) except that this entails boutons/terminals
hidden label: Remote axon only

Rod phenotype
type: Class
subclass of: Morphological phenotype
disjoint with: Spiny stellate phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Rod

Sensory phenotype
type: Class
subclass of: Phenotype
comment: the implementation of the sensor in a sensory neuron is essentially arbitrary with respect to subcompartment and projection pattern
hidden label: Sensory

Serotonergic phenotype
type: Class
subclass of: Expression phenotype
hidden label: Serotonergic

Slender phenotype
type: Class
subclass of: Trunk phenotype
disjoint with: Thick phenotype
comment: is this a synonym for narrow?
use object property: hasDendriteMorphologicalPhenotype
hidden label: Slender

Slender tufted pyramidal phenotype
type: Class
subclass of: Tufted pyramidal phenotype
disjoint with: Thick tufted pyramidal phenotype
comment: note that there is also an 'untufted slender' classification so we probably do need to break these out
use object property: hasMorphologicalPhenotype
hidden label: Slender tufted pyramidal

Small axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Small axon

Small basket phenotype
type: Class
subclass of: Basket phenotype
use object property: hasMorphologicalPhenotype
hidden label: Small basket

Small pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Star pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Small pyramidal

Soma morphological phenotype
type: Class
subclass of: Soma phenotype

Soma phenotype
type: Class
subclass of: Phenotype

Sparse axon phenotype
type: Class
subclass of: Axon phenotype
use object property: hasAxonMorphologicalPhenotype
hidden label: Sparse axon

Spiking phenotype
type: Class
subclass of: Electrophysiological phenotype
use object property: hasElectrophysiologicalPhenotype
hidden label: Spiking

Spinal cord ascending projection phenotype
type: Class
subclass of: Anterior projecting
comment: projects in the anterior direction of the spinal cord
use object property: hasProjectionPhenotype
hidden label: Spinal cord ascending projection

Spinal cord descending projection phenotype
type: Class
subclass of: Posterior projecting
comment: projects in the posterior direction of the spinal cord
use object property: hasProjectionPhenotype
hidden label: Spinal cord descending projection

Spiny phenotype
type: Class
subclass of: Dendrite phenotype
comment: Aspiny can be modelled as (not ilxtr:SpinyPhenotype), this will be needed for Allen's scheme
use object property: hasDendriteMorphologicalPhenotype
hidden label: Spiny

Spiny stellate phenotype
type: Class
subclass of: Morphological phenotype
subclass of: Spiny phenotype
disjoint with: Trilaminar phenotype
use object property: hasMorphologicalPhenotype
hidden label: Spiny stellate

Star pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Tufted pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Star pyramidal

Striato cortical
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Striato cortical

Sympathetic phenotype
type: Class
subclass of: Autonomic nervous system population phenotype
hidden label: Sympathetic

Thalamo cortical
type: Class
subclass of: Projection phenotype
use object property: hasProjectionPhenotype
hidden label: Thalamo cortical

Thick phenotype
type: Class
subclass of: Trunk phenotype
use object property: hasDendriteMorphologicalPhenotype
hidden label: Thick

Thick tufted pyramidal phenotype
type: Class
subclass of: Tufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Thick tufted pyramidal

Trilaminar phenotype
type: Class
subclass of: Morphological phenotype
use object property: hasMorphologicalPhenotype
hidden label: Trilaminar

Trunk phenotype
type: Class
subclass of: Dendrite phenotype
use object property: hasDendriteMorphologicalPhenotype
hidden label: Trunk

Tufted phenotype
type: Class
subclass of: Dendrite phenotype
comment: to get Untufted use the negative phenotype of this and add a naming rule
use object property: hasDendriteMorphologicalPhenotype
hidden label: Tufted

Tufted pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
disjoint with: Untufted pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Tufted pyramidal

Untufted pyramidal phenotype
type: Class
subclass of: Pyramidal phenotype
use object property: hasMorphologicalPhenotype
hidden label: Untufted pyramidal