Toward an Ontology for Neurons

From Program on Ontologies of Neural Structures

Toward an ontology of neurons

This document was started by Gordon Shepherd in February, 2010

The development of a systematic terminology for nerve cells is needed for building a comprehensive inventory of neurons and their properties in support of neuroscience research. Progress toward this goal is however hampered by the multiplicity of names for cells, and lack of a consensus on the criteria for defining neuron types. This review provides a brief background of the problems, and sets forth several proposals for solving them.

Background for naming nerve cells

The outward forms of nerve cells were first seen clearly using the silver impregnation method introduced by Camillo Golgi in the late 19th century. The Golgi method showed that in any given brain region the cells are divided into several distinct types characteristic for that region. The fundamental problem from the start was that the naming of these cell types and their parts was haphazard. In the cerebellum, for example, some types were eponymous (Purkinje cell, named after its discoverer, Jan Purkinje; Golgi cell, named after Golgi). Some were on the basis of size (granule cell, so-called because it appeared as small as a grain under the microscope). Some were named by the form of their axonal endings (mossy fiber, because of its mossy-looking terminal; climbing fiber, because it appeared to climb over the Purkinje cell dendritic tree), whereas some were named on the basis of their dendritic tree (stellate cell, because of its star-shaped dendritic tree emanating in all directions). The cell types in other regions suffered similar fates. By the early 20th century most of the main types of nerve cells had been described by the classical histologists, summarized in Ramon y Cajal's great work on the histology of the nervous system (1911). Although there was little logical basis for the terminology, the names stuck, and people simply got on with their studies using the names they preferred. Despite additions to the cell inventories since then, by the Golgi method and by a host of cell-specific markers in recent years, the same lack of rules for a systematic terminology has persisted.

Statement of the ontological problem

In our modern world this situation cannot persist. We communicate through digital machines and software which require agreement on the precise names for things. This has brought the field of ontology into neuroscience. The roots of ontology go back to the Greeks and the philosophy of meaning. For modern applications of ontology, we may simplify by consulting Wikipedia (where else in the modern sense would we turn?), where we find: "ontology deals with questions concerning what entities exist or can be said to exist, and how such entities can be grouped, related within a hierarchy, and subdivided according to similarities and differences."

This summarizes well the challenge in grappling with how to organize the terminology of neurons. A concerted attack on this problem is being carried out by the Neuroscience Information Framework (NIF) in concert with the International Neuroscience Coordinating Facility (INCF). Thus far four critical problems have been identified.

• First is to agree on a naming convention that identifies each cell type with its particular brain region, see Naming Convention
• Second is to agree on the specific criteria that must be met for a neuron to be of a given type, see Definition of Cell Type
• Third is to agree on the unambiguous term or terms for that type, see Neuron Registry Template
• Fourth is to identify any common features of any of the neuron types that will enable them to be grouped into families by "canonical" features.