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A Neuroinformatics of Brain Modeling and its Implementation in the Brain Operation Database BODB

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Abstract

We present principles for an integrated neuroinformatics framework which makes explicit how models are grounded on empirical evidence, explain (or not) existing empirical results and make testable predictions. The new ontological framework makes explicit how models bring together structural, functional, and related empirical observations. We emphasize schematics of the model’s operation linked to summaries of empirical data (SEDs) used in both the design and testing of the model, with tests comparing SEDs to summaries of simulation results (SSRs) from the model. We stress the importance of protocols for models as well as experiments. We complement the structural ontology of nested brain structures with a functional ontology of Brain Operating Principles (BOPs) for observed neural function and an ontological framework for grounding models in empirical data. We present an implementation of this ontological framework in the Brain Operation Database (BODB), an environment in which modelers and experimentalists can work together by making use of their shared empirical data, models and expertise.

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Acknowledgments

This work was supported in part by the National Science Foundation under Grant No. 0924674 as part of the University of Southern California Brain Project (USCBP). BODB was designed and implemented by many people under the leadership of Michael A. Arbib. Salvador Marmol designed ARDB (the Action Recognition Database), the precursor of BODB, and Rishabh Tandon updated it and released ARDB version 2.0. Anon Plangprasopchok took the lead in implementing the previous version of BODB for which Nantana Tinroongroj developed our first Talairach Applet. Implementation of the current version of BODB and development of BrainSurfer was primarily the work of James Bonaiuto. We thank Peter Fox and Jack Lancaster for making available the data from their Talairach Demon for our Talairach Applet (and now its extension in BrainSurfer), and David Marques of Elsevier and George Paxinos and Charles Watson for making portions of the electronic form for the Paxinos-Watson brain atlas of the macaque available for use in BrainSurfer.

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Authors and Affiliations

  1. USC Brain Project, Los Angeles, CA, USA

    Michael A. Arbib & James Bonaiuto

  2. Computer Science Department, University of Southern California, Los Angeles, CA, 90089-2520, USA

    Michael A. Arbib & Robert E. Schuler

  3. National Electronics and Computer Technology Center, Pathumthani, 12120, Thailand

    Anon Plangprasopchok

  4. Division of Biology, California Institute of Technology, Pasadena, CA, 91125, USA

    James Bonaiuto

Authors
  1. Michael A. Arbib
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  2. Anon Plangprasopchok
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  4. Robert E. Schuler
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Correspondence to Robert E. Schuler.

Appendix: Listing of Brain Operating Principles

Appendix: Listing of Brain Operating Principles

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Arbib, M.A., Plangprasopchok, A., Bonaiuto, J. et al. A Neuroinformatics of Brain Modeling and its Implementation in the Brain Operation Database BODB. Neuroinform 12, 5–26 (2014). https://doi.org/10.1007/s12021-013-9209-y

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