PT - JOURNAL ARTICLE AU - Heidi Kleven AU - Thomas H. Gillespie AU - Lyuba Zehl AU - Timo Dickscheid AU - Jan G. Bjaalie AU - Maryann E. Martone AU - Trygve B. Leergaard TI - AtOM, an ontology model for standardizing use of brain atlases in tools, workflows, and data infrastructures AID - 10.1101/2023.01.22.525049 DP - 2023 Jan 01 TA - bioRxiv PG - 2023.01.22.525049 4099 - http://biorxiv.org/content/early/2023/01/23/2023.01.22.525049.short 4100 - http://biorxiv.org/content/early/2023/01/23/2023.01.22.525049.full AB - 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.Competing Interest StatementMM is the founder and has equity interest in SciCrunch Inc, a tech start up out of UCSD that provides tools and services in support of reproducible science and Research Resource Identifiers. JGB is a member of the Management Board of the EBRAINS AISBL, Brussels, Belgium. The other authors declare that no competing interests or conflicts of interest exist for any of the authors.