A taxonomy of phenotypes used to model biological types as collections of measurements.
Autonomic nervous system population phenotype
used to account for populations that are part of distinct autonomic nervous system subdivisions
projects in the anterior direction of the housing structure
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.
figure out how to regularize these since I have used ilxtr:parvalbumin elsewhere, probably ilxtr:phenotype/thing will be best
Early bifurcating thick tufted pyramidal phenotype
Early bifurcating thick tufted pyramidal
Early bifurcating tufted pyramidal phenotype
we are not modelling dendrite phenotypes directly at the moment so we cant break about EB/LB
this is the 'general' morphological phenotype that might be made up of soma/axon/dendrite
local projections only? (define local) equivalent to LocalAxonOnly, is this an axon phenotype or an axon location phenotype?
Late bifurcating thick tufted pyramidal phenotype
Late bifurcating tufted pyramidal phenotype
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
we really should be able to deal with spines in a convenient way
motor neuron phenotype, motor projecting phenotype, muscle projecting phenotype, hasForwardConnectionPhenotype some myocyte, implies
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)
this class is circumspect, and may actually be NarrowTuftedPyramidalPhenotype
Parasympathetic Post-Ganglionic phenotype
Parasympathetic Pre-Ganglionic phenotype
Petilla initial classical spiking phenotype
Petilla initial delayed spiking phenotype
Petilla sustained accommodating phenotype
how do we deal with the fact that there are other accommodating phenotypes‚ multiple parent is annoying
Petilla sustained non accommodating phenotype
projects in the posterior direction of the housing structure
we don’t always have target location information, sometimes the best we get is ‘the axon leaves the section’, equivalent to RemoteAxon
hasProjectionPhenotype (some (class brainRegion (not (brainRegion containing this neruon))))
model this as NegPhenotype(ilxtr:LocalAxon) except that this entails boutons/terminals
the implementation of the sensor in a sensory neuron is essentially arbitrary with respect to subcompartment and projection pattern
note that there is also an 'untufted slender' classification so we probably do need to break these out
Spinal cord ascending projection phenotype
projects in the anterior direction of the spinal cord
Spinal cord descending projection phenotype
projects in the posterior direction of the spinal cord
Aspiny can be modelled as (not ilxtr:SpinyPhenotype), this will be needed for Allen's scheme
to get Untufted use the negative phenotype of this and add a naming rule