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@ARTICLE{Kleven:1007218,
      author       = {Kleven, Heidi and Gillespie, Thomas H. and Zehl, Lyuba and
                      Dickscheid, Timo and Bjaalie, Jan G. and Martone, Maryann E.
                      and Leergaard, Trygve B.},
      title        = {{A}t{OM}, an ontology model for standardizing use of brain
                      atlases in tools, workflows, and data infrastructures},
      journal      = {bioarxiv},
      reportid     = {FZJ-2023-01990},
      pages        = {24},
      year         = {2023},
      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.},
      cin          = {INM-1},
      cid          = {I:(DE-Juel1)INM-1-20090406},
      pnm          = {5254 - Neuroscientific Data Analytics and AI (POF4-525) /
                      HBP SGA2 - Human Brain Project Specific Grant Agreement 2
                      (785907) / HBP SGA3 - Human Brain Project Specific Grant
                      Agreement 3 (945539) / HIBALL - Helmholtz International
                      BigBrain Analytics and Learning Laboratory (HIBALL)
                      (InterLabs-0015)},
      pid          = {G:(DE-HGF)POF4-5254 / G:(EU-Grant)785907 /
                      G:(EU-Grant)945539 / G:(DE-HGF)InterLabs-0015},
      typ          = {PUB:(DE-HGF)25},
      doi          = {10.1101/2023.01.22.525049},
      url          = {https://juser.fz-juelich.de/record/1007218},
}