AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures

Abstract

Brain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.

Fig. 1

Atlas Ontology Model elements. (a-b) The elements of a fictional two-dimensional brain atlas illustrated using a coronal Nissl-stained section and a drawing of the Platypus (ornithorhynchus anatinus) brain. (c) The Atlas Ontology Model, formalizing the elements of a reference atlas.

Fig. 2

The relations and metadata of the AtOM elements. (a) Diagram illustrating the relations between the AtOM elements: measures (to provide a metric to), parameterizes (to set the conditions of its operation) and identifies (to recognize, establish or verify the identity of something). Thus, the coordinate system measures the reference data and annotation set with coordinates as units. The terminology identifies the annotation set and coordinate system with terms as units. The reference data and the annotation set provide physical dimensions embodying the coordinate system and the terminology. The model consists of two reference modules: spatial (containing the coordinate system and reference data, yellow) and semantic (containing annotations and terminology, blue). Each element can be one of a set of alternatives (b), which have a set of metadata (c). (d) Key for reading the figure.

Fig. 3

AtOM elements illustrated for three brain atlas versions. (a–c) Tabular illustration of the most recent versions of (a) the Allen Mouse Brain Atlas Common Coordinate Framework, (b) the Waxholm Space atlas of the Sprague Dawley rat brain and, (c) one alternative representation of the Julich-Brain cytoarchitectonic atlas organized in accordance with the AtOM diagram (top row). All atlases are accessible in the EBRAINS research infrastructure. Specification of the metadata, licenses and versions of these atlases are given in Tables 1, 2. CCF, Common Coordinate Framework; AMRA, Allen Mouse Reference Atlas; WHS, Waxholm Space; MNI, Montreal Neurological Institute; PM, probabilistic maps; MPM, maximum probability maps.