cell type terms request for NPO

[tgbugs]

• basket cell (cl has this one but the definition is bad)
• calbindin neuron hasPhenotype some 'Calb (indicator)'
• calretnin neuron hasPhenotype some 'Calb2 (indicator)'
• cerebellar interneuron hasPhenotype some 'Intrinsic phenotype' and hasPhenotype some ('part of' some cerebellum) (possibly leave this one out?)
• cck+ hasPhenotype some 'Cck (indicator)'
• chat+ hasPhenotype some 'ACh (indicator)' sort of, but want chat+ only not the other indicator subclasses?
• cholinergic interneuron? http://uri.interlex.org/npo/uris/neurons/34 ?? may be sufficient?
• cholinergic neuron http://uri.interlex.org/base/ilx_0102131 vs http://uri.interlex.org/base/ilx_0784333, do we need an unqualified version of this? just subclass of Neuron instead of NeuronCUT?
• cortical interneuron hasPhenotype some 'Intrinsic phenotype' and hasPhenotype some ('part of' some neocortex) (don't add this one because of issues with usage for cortical usually implying neocortical and the fact that data annotation should use intrinsic neuron + the most granular brain region available)
• dopaminergic neuron needs help http://uri.interlex.org/base/ilx_0103395 because the indicators are currently disjoint TH+ exists but DA+ does not
• excitatory neuron needs modelling, excitatory phenotype is not modelled at all, and excitatory neurotransmitter is not disjoint with inhibitory neurotransmitter hasPhenotype some Excitatory
• fast spiking neuron hasPhenotype some 'Fast spiking phenotype' and hasPhenotype some 'Intrinsic phenotype' issue with petilla vs other definitions of fast spiking
• granule neuron hasPhenotype some 'Granule phenotype'
• inhibitory neuron hasPhenotype some Inhibitory needs modelling
• interneuron http://uri.neuinfo.org/nif/nifstd/nlx_cell_1003113 should work, but need to review modelling of hasInstanceInTaxon axioms in the equivalent class, probably want to convert this to subClassOf hasInstanceInTaxon metazoa
• motor neuron hasPhenotype some 'Motor phenotype'
• npy neuron hasPhenotype some 'Npy (indicator)'
• nos neuron hasPhenotype some 'Nos1 (indicator)'
• pv neuron hasPhenotype some 'parvalbumin (indicator)'
• postmitotic cell, likely a superclass of neuron, not clear whether this is useful since all neurons are by definition post mitotic, and the usage in this case may be to clearly distinguish from neuronal precursor cells that might be referred to as "neurons" in some cases
• 'neural progenitor cell' CL:0011020
• pyramidal neuron hasPhenotype some 'Pyramidal phenotype'
• sensory neuron hasPhenotype some 'Sensory phenotype'
• sst+ neuron hasPhenotype some 'somatostatin (indicator)'
• spinal interneuron (possibly leave this one out?)
• spiny neuron NLXCELL:100601 only in ontology hasPhenotype some 'Spiny phenotype'
• stellate neuron missing cell phenotype class using PATO I think
• striatum interneuron hasPhenotype some ('part of' some striatum) and hasPhenotype some 'Intrinsic phenotype' (possibly leave out?)
• http://purl.obolibrary.org/obo/CL_0000359
• vip neuron hasPhenotype some 'VIP (indicator)'
• cortical neuron hasPhenotype some ('part of' some 'cerebral cortex') includes hippocampus, but also need to check whether people actually mean neocortical neuron because piriform cortex and hippocampus are usually explicitly differentiated, not a good term for annotation because its use is ambiguous (would rather not create for annotation purposes)
• layer 6 neuron hasPhenotype some ('part of' some 'cortical layer VI') (possibly leave out?)
• D1 receptor expressing neuron hasPhenotype some 'Drd1 (indicator)'
• D2 receptor expressing neuron hasPhenotype some 'Drd2 (indicator)'
• aromatase expressing neuron needs a phenotype indicator https://en.wikipedia.org/wiki/Aromatase
• olfactory bulb tufted cell have two subclasses that need a common parent
• zinc releasing neuron this needs quite a bit of modelling to determine transmitter vs modulator and hasSynapticVesiclePhenotype or something similar

[tgbugs]

https://github.com/HumanBrainProject/openMINDS_controlledTerms/issues/297 https://github.com/HumanBrainProject/openMINDS_controlledTerms/issues/240 https://github.com/HumanBrainProject/openMINDS_controlledTerms/issues/257