Naming Convention
From Program on Ontologies of Neural Structures
Naming convention
Begin with the brain region.
The first problem is the easiest and in certain ways the necessary place to start. We recognize to begin with that neuron cell bodies are located in specific regions of the nervous system. This means that the name for all the cells in a given region must start with the name of that region. For example, a ganglion cell in the retina must have as its name Retina Ganglion Cell. It will not do to lump it together with any other cell that happens to have that unhelpful name of "ganglion cell", which has no meaning other than that its discoverer just called it by a generic name signifying "large". In this way, we group all the different types of cells in the retina as "Retina", followed by the common name for the different types. In other words, all of these cells belong to the class "Retina". The same applies to every other cell in the nervous system. Such a convention can be characterized by "Region Cell Name". We thus avoid distributing the cells of a given region haphazardly throughout an alphabetical inventory list, i.e., granule cells of the cerebellum, olfactory bulb, dentate gyrus, etc, all grouped together simply by the name "granule".
This convention of Region Cell Name has to subsume several possible complications. First, there may be several parts to the cell region. For example, the cochlear nucleus has dorsal and ventral parts that are distinct in their cell types and functions. Although we refer to them colloquially as the dorsal cochlear nucleus and ventral cochlear nucleus, for the purposes of listing them they must follow a parent-child convention to keep them together, thus, Cochlear Nucleus Dorsal and Cochlear Nucleus Ventral, plus in each case the cell name (i.e. Cochlear Nucleus Dorsal Fusiform Cell and Cochlear Nucleus Ventral Bushy Cell). Similarly, Olfactory Bulb Main Mitral Cell and Olfactory Bulb Accessory Mitral Cell. Thus, we have the expanded parent-child convention "Region Subregion Cell Name". This naming convention it should be stressed is specifically for constructing an alphabetically-arranged list of cell names; colloquially we of course continue to use their common names in their common order, i.e. a "mitral cell of the main olfactory bulb", etc.
Further complexities apply to cortical regions because of their laminar characteristic. However, these are also accomodated by an expansion of the parent-child relation; thus, a cortical pyramidal cell in lamina 3 of the motor cortex is termed "Neocortex Motor Layer 3 Pyramidal Cell".
The utility of this approach has been tested on 160 neuron types in the list under "neuron" in the Neurolex Vocabulary of the NIF website. This naming convention provides the basis for the next steps in solving the other three problems terminology problems mentioned above.
It should be noted that we assume we are dealing with the mammalian nervous system. The same approach can be used for any species in which the cell type is unique or different from the general mammalian pattern, or for any species vertebrate or invertebrate. In those cases, an additional initial species modifier is needed to make this clear.
