BAMS Neuroanatomical Ontology: Design and Implementation

Abstract

We describe in this paper the structure and main features of a domain specific ontology for neuroscience, the BAMS Neuroanatomical Ontology. The ontology includes a complete set of concepts that describe the parts of the rat nervous system, a growing set of concepts that describe neuron populations identified in different brain regions, and relationships between concepts. The ontology is linked with a complex representation of structural and physiological variables used to classify neurons, which is encoded in BAMS. BAMS Neuroanatomical Ontology is accessible on the web and includes an interface that allows browsing terms, viewing criteria for classification, and accessing associated information.

Keywords: BAMS; neuron classification; ontology; rat; structural neuroanatomy.

Figure 1

The OR schema of BAMS Neuroanatomical Ontology.

Figure 2

The general structure of BAMS Neuroanatomical Ontology.

Figure 3

Schema of classification criteria associated with “is-a” relations between neurons in BAMS Neuroanatomical Ontology.

Figure 4

The web interface of BAMS Neuroanatomical Ontology allows users to browse concepts and retrieve their definitions, defining nomenclatures, parents and children, and synonyms.

Figure 5

BAMS Neuroanatomical Ontology web interface allows users to view those brain regions where the neuron type or class of interest was identified. Links are associated with each brain region abbreviation, and they return descriptions of the regions, as recorded in BAMS (Bota et al., ; Bota and Swanson, 2006).

Figure 6

Information that can be retrieved in BAMS and is related to neuron concepts include related terms, their semantic relations, annotations, references and collators, as well as the set of parents with links to the associated classification criteria. The neuron type “C others” defined in the nomenclature “Huxlin & Goodchild” (Huxlin and Goodchild, 1997) has two related terms in BAMS Neuroanatomical Ontology: it includes the retinal ganglion cell type III, nomenclature Perry (Perry, 1979) and has as synonym the retinal ganglion cell C3, nomenclature Sun (Sun et al., 2004).

Figure 7

Users can access classification criteria associated with each “is a” relationship included in BAMS Neuroanatomical Ontology. Retrieved criteria are organized as ordered lists of variables used to define and classify the neuron concepts. Associated information includes textual annotations, references, and collator names. The list of variables shown in this Figure is used to classify rat retinal ganglion cells A2 inner (Huxlin and Goodchild, 1997) as projection interneurons, passing through the intermediary classes.