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.

Details

Title
AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures
Author
Kleven, Heidi 1   VIAFID ORCID Logo  ; Gillespie, Thomas H. 2 ; Zehl, Lyuba 3   VIAFID ORCID Logo  ; Dickscheid, Timo 4 ; Bjaalie, Jan G. 1   VIAFID ORCID Logo  ; Martone, Maryann E. 2   VIAFID ORCID Logo  ; Leergaard, Trygve B. 1   VIAFID ORCID Logo 

 University of Oslo, Department of Molecular Medicine, Institute of Basic Medical Sciences, Oslo, Norway (GRID:grid.5510.1) (ISNI:0000 0004 1936 8921) 
 University of California, Department of Neurosciences, San Diego, USA (GRID:grid.266100.3) (ISNI:0000 0001 2107 4242) 
 Research Centre Jülich, Institute of Neuroscience and Medicine (INM-1), Jülich, Germany (GRID:grid.8385.6) (ISNI:0000 0001 2297 375X) 
 Research Centre Jülich, Institute of Neuroscience and Medicine (INM-1), Jülich, Germany (GRID:grid.8385.6) (ISNI:0000 0001 2297 375X); Heinrich Heine University Düsseldorf, Institute of Computer Science, Düsseldorf, Germany (GRID:grid.411327.2) (ISNI:0000 0001 2176 9917) 
Pages
486
Publication year
2023
Publication date
2023
Publisher
Nature Publishing Group
e-ISSN
20524463
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2842279752
Copyright
© The Author(s) 2023. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.