AtOM, an ontology model for standardizing 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 standardization 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 propose minimum requirements for FAIR atlases and discuss how AtOM may facilitate atlas interoperability and data integration. 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.

A neuroscientist’s guide to using murine brain atlases for efficient analysis and transparent reporting

“…The most detailed and commonly used volumetric atlas for the mouse is the Allen Mouse Brain Common Coordinate Framework (Allen Mouse Brain CCF; Wang et al, 2020 ), which has been instrumental for the acquisition and sharing of the Allen Institute’s large data collections ( Lein et al, 2007 ; Oh et al, 2014 ; Tasic et al, 2016 ). For the rat, the most detailed volumetric atlas is the Waxholm Space atlas of the Sprague Dawley rat brain (WHS rat brain atlas; RRID:SCR_017124 ; Papp et al, 2014 ; Kjonigsen et al, 2015 ; Osen et al, 2019 ; Kleven et al, 2023a ). Other murine brain atlases are also available [see summary by Barrière et al (2019) ].…”

“…Other murine brain atlases are also available [see summary by Barrière et al (2019) ]. Regardless of the 2D or 3D format, murine brain atlases can be navigated and interpreted using the spatial, visual, and semantic reference space ( Figure 1A ; Kleven et al, 2023a ).…”

“… Navigating brain atlases to find anatomical locations. (A) Simplified version of the brain atlas ontology model (AtOM, Kleven et al, 2023a ). The main elements of an atlas include the coordinate system, the reference image (here exemplified with a coronal platypus brain section; Mikula et al, 2007 ), the annotated brain regions, and the brain region names.…”

“…However, volumetric digital atlases are often provided with several files that may be versioned separately. To facilitate correct citation, Kleven et al (2023a) proposed an Atlas ontology model and an overview of the versioning of the two most commonly used volumetric murine brain atlases, the WHS rat brain atlas and the Allen Mouse Brain CCF. Beyond consistent and correct citation of atlases, any customizations (see “Customizing brain atlases for analysis and visualization”) should be clearly documented ( Rodarie et al, 2021 ).…”

“…As these examples show, several atlases are required to cater to current needs, and future methodologies and findings will add further possibilities and needs for continued development and refinement of atlases. For such new atlases to enable researchers to cite, (re-)analyze, and compare data independently of the original atlas used, it is essential that they are openly shared and properly documented ( Kleven et al, 2023a ).…”