An ontology of neuron types based on the phenotypic dimensions of cells that can be measure experimentally.
Mohameth François Sy - https://orcid.org/0000-0002-4603-9838
Shreejoy Tripathy - https://orcid.org/0000-0002-1007-9061
Maryann Martone - https://orcid.org/0000-0002-8406-3871
Tom Gillespie - https://orcid.org/0000-0002-7509-4801
researchers working on cell types and their phenotypes, whether they are collecting raw data, organizing existing data, or creating simulations of cell types
`npokb:' and `ilxtr:' identifiers are not currently dereferenceable, but they are planned to be.
Protégé, FaCT++, ELK, python, pyontutils, neurondm
Specific ontology ids are never deprecated. If you need to know whether the modeling of a class has changed, neurondm can be used to regenerate the deterministic identifiers that appear as `ilxtr:hasTemporaryId'.
`rdfs:label' must be present. `skos:prefLabel' must be present for common usage types, and should be present when possible for evidence based models. Since the constituent ontology files that make up the npo are generated using python, provenance is primarily stored in the git repository pointed to via the `prov:wasGeneratedBy' predicate in the `owl:Ontology' header for individual files, in this case that repository is `<https://github.com/tgbugs/pyontutils>'
`rdfs:label' must be automatically generated using neurondm. Labels are generated from the labels of the constituent phenotype values. Only restrictions specifying necessary criteria for defining the type (i.e. those that are contained in an `owl:equivalentClass' statement) are included when generating the name. The ordering of the dimensions is specified in https://github.com/tgbugs/pyontutils/blob/a5e9fcc70d56870e692c17cb7fadce735a281d02/neurondm/neurondm/core.py#L135-L389
No external evaluation has been conducted. See TODO-preprint
`npokb:[0-9]+' identifiers are assigned sequentially via https://github.com/tgbugs/pyontutils/blob/a5e9fcc70d56870e692c17cb7fadce735a281d02/nifstd/nifstd_tools/map-identifiers.py#L20-L49. An index of issued identifiers is retained at https://github.com/SciCrunch/NIF-Ontology/blob/neurons/ttl/generated/neurons/npokb-index.ttl. Note that the current implementation currently does not correctly handles cases where the constituent phenotypes of a class change.
There is a need to bridge the gap between historical definitions of cell types from the literature, with cell types being defined using a wide variety of new techniques. There is also a need to be able to bridge and reconcile the wide variety of local terminology used across laboratories and place them on more solid foundations derived from the methodology used to make measurements on cells.
Scope: neuron types, and the dimensions and values of their constituent phenotypes. Coverage: an inventory of common usage types from existing sources, as well as three examples of evidence based models of cell types from recent publications.
The npo is maintained as part of the NIF-Ontology.
See `MIRO:axiom_patterns' and paper TODO-preprint
Development versions of the ontology are released continuously and are identified by their git commit hashes. Stable versions are released periodically and can be accessed by their git tag.
L-Cysteinyl-L-tyrosyl-L-isoleucyl-L-glutaminyl-L-asparaginyl-L-cysteinyl-L-prolyl-L-leucylglycinamide cyclic(1-6)-disulfide
6-O-[(11E)-3-hydroxy-2-tetradecyloctadec-11-enoyl]-alpha-D-glucopyranosyl alpha-D-glucopyranoside
carbohydrates and carbohydrate derivatives
dicarboxylic acids and O-substituted derivatives
acetylcholine receptor, neuronal, nicotinic, alpha-4 subunit
cholinergic receptor, nicotinic, alpha polypeptide 4
neuronal acetylcholine receptor subunit alpha-4
ca(2+)/calmodulin-activated adenylyl cyclase
solute carrier family 7 (cationic amino acid transporter, y+ system), member 3
vitamin D-dependent calcium-binding protein, avian-type
calcitonin/calcitonin-related polypeptide, alpha
cholinergic receptor, muscarinic 3, cardiac
striatal cannabinoid receptor type 1 protein
gamma-aminobutyric acid (GABA) A receptor, subunit alpha 1
gamma-aminobutyric acid receptor subunit alpha-1
gamma-aminobutyric acid (GABA) A receptor, subunit alpha 4
gamma-aminobutyric acid receptor subunit alpha-4
gamma-aminobutyric acid (GABA) A receptor, subunit delta
gamma-aminobutyric acid receptor subunit delta
glutamate receptor, ionotropic, AMPA1 (alpha 1)
glutamate receptor, ionotropic, AMPA4 (alpha 4)
5-hydroxytryptamine (serotonin) receptor 2C
5-hydroxytryptamine (serotonin) receptor 3A
5-hydroxytryptamine (serotonin) transporter
Sodium-dependent serotonin transporter (5HT transporter) (5HTT)
solute carrier family 6 (neurotransmitter transporter, serotonin), member 4
N-ethylmaleimide sensitive fusion protein
suppressor of K(+) transport growth defect 2
calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A
phosphodiesterase 1A, calmodulin-dependent
cAMP-specific 3',5'-cyclic phosphodiesterase 4B
nuclear receptor subfamily 1 group C member 3
peroxisome proliferator activated receptor gamma
peroxisome proliferator activated receptor gamma 2
peroxisome proliferator activated receptor gamma 4
peroxisome proliferator-activated receptor gamma
peroxisome proliferative activated receptor, gamma, coactivator 1 alpha
peroxisome proliferator-activated receptor gamma coactivator 1-alpha
heparin-binding growth-associated molecule
retinally abundant regulator of G-protein signaling
solute carrier family 18 (vesicular monoamine), member 3
downregulated during adipocyte differentiation-1
transforming growth factor beta-3 proprotein
short transient receptor potential channel 5
transient receptor potential cation channel, subfamily C, member 5
vtransient receptor potential cation channel, subfamily C, member 5
short transient receptor potential channel 6
transient receptor potential cation channel, subfamily C, member 6
solute carrier family 32 (GABA vesicular transporter), member 1
vasicular inhibitory amino acid transporter 10D
vesicular inhibitory amino acid transporter
pituitary adenylate cyclase-activating polypeptide type II receptor
vasoactive intestinal peptide receptor 1
vasoactive intestinal polypeptide receptor 1
pituitary adenylate cyclase-activating polypeptide type III receptor
vasoactive intestinal peptide receptor 2
vasoactive intestinal polypeptide receptor 2
wingless-related MMTV integration site 2
wingless-type MMTV integration site family, member 2
wingless-related MMTV integration site 5A
wingless-type MMTV integration site family, member 5A
Regulator of G-protein signaling 7 (RGS7)
nuclear receptor subfamily 3 group B member 3
cAMP-specific 3',5'-cyclic phosphodiesterase 7B
guanylate cyclase soluble subunit beta-1
guanylate cyclase soluble subunit beta-3
NO-sensitive guanylyl cyclase beta 1 subunit
soluble guanylate cyclase beta-1 subunit
calcium-activated potassium channel subunit beta-4
calcium-activated potassium channel, subfamily M subunit beta-4
large conductance calcium-dependent potassium ion channel beta 4 subunit
potassium large conductance calcium-activated channel, subfamily M, beta member 4
guanylate cyclase soluble subunit alpha-1
guanylate cyclase soluble subunit alpha-3
striatum-specific G-protein coupled receptor
calcium-activated potassium channel subunit beta-2
calcium-activated potassium channel, subfamily M subunit beta-2
potassium large conductance calcium-activated channel, subfamily M, beta member 2
carbohydrate (keratan sulfate Gal-6) sulfotransferase 1
galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 1
N-acetylglucosamine-6-O-sulfotransferase 1
differentiation-associated Na(+)-dependent inorganic phosphate cotransporter
solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6
solute carrier family 17 (vesicular glutamate transporter), member 6
cysteine-rich and single thrombospondin domain-containing protein 3
thrombospondin type 1 domain containing gene Rspondin
cGMP-dependent 3',5'-cyclic phosphodiesterase
rho guanine nucleotide exchange factor 10
Rho guanine nucleotide exchange factor (GEF) 10
cysteine-rich and single thrombospondin domain-containing protein 2
dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11A
cGMP-binding cGMP-specific phosphodiesterase
cGMP-specific 3',5'-cyclic phosphodiesterase
cholinergic receptor, muscarinic 2, cardiac
Ca(2+)/calmodulin-activated adenylyl cyclase
heparan sulfate (glucosamine) 3-O-sulfotransferase 4
heparan sulfate glucosamine 3-O-sulfotransferase 4
Hyperpolarization and cyclic-nucleotide gated channel
Anionic cys-loop ligand-gated ion channel
Cationic cys-loop ligand-gated ion channel
NMDA-type glutamate-gated cationic channel
AMPA-type glutamate-gated cationic channel
Kainate glutamate-gated cationic channel
Olfactory bulb main external plexiform layer
Olfactory bulb (main) internal plexiform layer
Olfactory bulb (accessory) external plexiform layer
multiply inhering quality of a physical entity
potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel protein
rhodopsin-like G-protein coupled receptor
growth hormone release-inhibiting factor
L-Tyrosine, tetrahydrobiopterin:oxygen oxidoreductase (3-hydroxylating)
parasympathetic part of autonomic division of nervous system
pars parasympathica divisionis autonomici systematis nervosi
somatic nervous system, somatic division
somatic part of peripheral nervous system
camera-type eye plus associated structures
spinal ganglion part of peripheral nervous system
proximo-distal subdivision of respiratory tract
tubular parts of female reproductive system
cranial ganglion part of peripheral nervous system
cochlear nucleus of eighth cranial nerve
interstitial nucleus of stria terminalis
nucleus interstitialis striae terminalis
nucleus proprius stria terminalis (bed nucleus)
medial geniculate complex of dorsal thalamus
paraventricular nucleus hypothalamus (Malone)
paraventricular nucleus of the hypothalamus
strata (grisea et alba) colliculi cranialis
strata (grisea et alba) colliculi superioris
nucleus rotundus subthalamo-peduncularis
nucleus substantiae nigrae, pars compacta
nucleus substantiae nigrae, pars reticularis
pseudostratified main olfactory epithelium
nucleus pigmentosus subthalamo-peduncularis
nucleus fasciculi longitudinalis medialis
nucleus of the posterior commissure (Darkschewitsch)
superior olivary nucleus (Barr & Kiernan)
median eminence of posterior lobe of pituitary gland
columna grisea anterior medullae spinalis
periventricular zone of the hypothalamus
hypothalamic medial zone behavioral control column
cytoarchitectural fields of hippocampal formation
autonomic division of peripheral nervous system
autonomic part of peripheral nervous system
divisio autonomica systematis nervosi peripherici
pars autonomica systematis nervosi peripherici
white matter structure of cerebral hemisphere
medial globus pallidus (entopeduncular nucleus)
interstitial nucleus of medial longitudinal fasciculus
interstitial nucleus of medial longitudinal fasciculus (Crosby)
interstitial nucleus of the medial longitudinal fascicle (Boyce 1895)
interstitial nucleus of the medial longitudinal fasciculus
nucleus of the posterior commissure (Kvlliker)
principal sensory nucleus of trigeminal nerve
nucleus sensibilis superior nervi trigemini
nucleus sensorius principalis nervi trigemini
nucleus sensorius superior nervi trigemini
principal sensory nucleus of the trigeminal
principal sensory nucleus of the trigeminal nerve
trigeminal nerve superior sensory nucleus
nucleus lemnisci lateralis pars ventralis
nucleus of the lateral lemniscus ventral part
nucleus of the lateral lemniscus, ventral part
ventral nucleus of the lateral lemniscus
formatio reticularis tegmenti mesencephali
geniculate thalamic nuclear group (metathalamus)
lateral nuclear group of dorsal thalamus
dorsal spinocerebellar tract of the medulla
inferior olivary complex dorsalaccessory nucleus
nucleus nervi oculomotorii, pars medialis
vestibular part of vestibulocochlear ganglion
vestibulocochlear ganglion vestibular component
vestibulocochlear VIII ganglion vestibular component
nucleus nervi oculomotorii ventrolateralis
nucleus nervi oculomotorii, pars ventralis
arcuate hypothalamic nucleus medial part
arcuate nucleus of hypothalamus of medulla
arcuate periventricular nucleus of medulla
infundibular hypothalamic nucleus of medulla
infundibular periventricular nucleus of medulla
medulla infundibular hypothalamic nucleus
medulla infundibular periventricular nucleus
dorsal motor nucleus of the vagus (vagal nucleus)
nucleus parvocellularis nervi hypoglossi
medial amygdaloid nucleus principal part
nucleus tractus mesencephali nervi trigeminalis
ventral nucleus of oculomotor nuclear complex
superior olivary complex periolivary region
Purkinje cell layer of cerebellar cortex
lateral posterior nucleus of the thalamus
substantia grisea centralis mesencephali
cytoarchitectural part of olfactory bulb
cytoarchitectural part of the cerebellar cortex
olfactory bulb main mitral cell body layer
columna grisea intermedia medullare spinalis
septum pellucidum of telencephalic ventricle
mucosa of organ of apparatus respiratorius
mucous membrane of apparatus respiratorius
apparatus respiratorius epithelial tissue
epithelial tissue of apparatus respiratorius
epithelial tissue of upper respiratory tract
upper respiratory tract epithelial tissue
ventricular system of central nervous system
region of wall of ventricular system of neuraxis
external plexiform layer of the olfactory bulb
olfactory bulb main external plexiform layer
accessory olfactory bulb granule cell layer
lamina molecularis isocorticis [lamina I]
external granular layer of cerebral cortex
external granular layer of isocortex [layer II]
external granule cell layer of neocortex
lamina granularis externa isocorticis [lamina ii]
external pyramidal cell layer of neocortex
external pyramidal layer of cerebral cortex
external pyramidal layer of isocortex [layer iii]
isocortex, deep supragranular pyramidal layer
lamina pyramidalis externa isocorticis [lamina iii]
layer of medium-sized and large pyramidal cells
internal granular layer of isocortex [layer iv]
internal granule cell layer of neocortex
lamina granularis interna isocorticis [lamina iv]
internal pyramidal cell layer of neocortex
internal pyramidal layer of isocortex [layer v]
isocortex, infragranular pyramidal layer
lamina pyramidalis interna isocorticis [lamina v]
lamina multiformis isocorticis [lamina vi]
segmenta sacralia medullae spinalis [1-5]
pars basolateralis (Corpus amygdaloideum)
corpus amygdaloideum pars corticomedialis
pars corticomedialis (Corpus amygdaloideum)
cytoarchitectural part of superior colliculus
predominantly white regional part of superior colliculus
white matter layer of superior colliculus
visual processing part of nervous system
accessory olfactory bulb glomerular layer
accessory olfactory bulb, glomerular layer
glomerular layer of the accessory olfactory bulb
hippocampus stratum lacunosum moleculare
stratum hippocampi moleculare et substratum lacunosum
primary somatosensory cortex (area S1, areas 3,1,2)
nucleus tractus solitarii medullae oblongatae
structure with developmental contribution from neural crest
pseudostratified ciliated columnar epithelium
epithelium pseudostratificatum columnare ciliatum (trachea et bronchi)
primary subdivision of cranial skeletal system
anterior division of bed nuclei of stria terminalis
anterior part of the bed nucleus of the stria terminalis
bed nuclei of the stria terminalis anterior division
bed nuclei of the stria terminalis, anterior division
bed nuclei of the stria terminals anterior division
bed nucleus of the stria terminalis anterior division
bed nucleus of the stria terminalis anterior part
bed nucleus of thestria terminalis anterior division
central nervous system cell part cluster
predominantly white regional part of telencephalon
predominantly gray regional part of telencephalon
subdivision of organism along main body axis
CA1 part of stratum pyramidale hippocampi
CA2 part of stratum pyramidale hippocampi
CA3 part of stratum pyramidale hippocampi
CA1 part of stratum lacunosum moleculare
stratum lacunosum moleculare of the CA1 field
CA3 part of stratum lacunosum moleculare
stratum lacunosum moleculare of the CA3 field
accessory olfactory bulb, granular layer
accessory olfactory bulb mitral cell layer
gray matter of lobe of cerebral hemisphere
central nervous system gray matter layer
central nervous system white matter layer
posterior column-medial leminscus pathway
posterior column-medial lemniscus system
posterior column/medial leminscus pathway
predominantly white regional part of pontine tegmentum
molecular layer of dorsal cochlear nucleus
inner layer of dentate gyrus molecular layer
organ region with floating fiat boundary