Table 1.
The current Phenotypic Dimensions of the NPO and the associated ontologies/vocabularies used to populate the data model. When NIFSTD appears in this table the terms were nearly always added to support the NPO. Examples are drawn from Fig. 2
| Phenotypic dimension | Definition | Vocabularies/ontologies |
|---|---|---|
|
Taxonomic Example: Species |
The species or taxon rank in which the phenotype inheres | NCBI taxonomy1 |
|
Anatomical Example: Brain Region |
The regions of the nervous system containing parts of the neuron. Primary location is indicated by the location of the cell soma, but anatomical location may be assigned to any cell part through a series of predicates | UBERON; various brain atlases via NIFSTD parcellation2 |
| Morphological | Distinguishing morphological characteristics | NIFSTD3 |
|
Molecular Example: Expression |
Distinguishing molecular constituents | NCBI Gene4, CHEBI5, Protein Ontology6 |
| Physiological | Expresses a relationship between a neuron type and an electrophysiological phenotype concept. This should be used when a neuron type is described using a high level electrophysiological concept class, e.g., bursting | NIFSTD Petilla Conventions (Petilla Interneuron Nomenclature Group, 2008) |
| Connection | Indicates a synaptic relationship between cell types. Further elaborated into connectivity determined by different techniques, e.g., physiology, electron microscopy | Gene Ontology7 |
|
Circuit role Example: Projection |
Indicates whether the neuron is an Intrinsic neuron (local circuit neuron), projection neuron, or sensory neuron | NIFSTD (Bug et al., 2008) |
|
Projection targets Example: Projection |
Expresses a relationship between a neuron type and a brain region to which it sends axons. Synaptic relationships are represented through the connection relationship | UBERON (Mungall et al., 2012)/various atlases/NIF Gross Anatomy (Bug et al., 2008) |