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

Arbib, Michael A. and Plangprasopchok, Anon and Bonaiuto, James and Schuler, Robert E. (2014) A Neuroinformatics of Brain Modeling and its Implementation in the Brain Operation Database BODB. Neuroinformatics, 12 (1). pp. 5-26. ISSN 1539-2791.

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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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Additional Information:© 2013 Springer Science+Business Media New York. Published online: 15 November 2013. 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.
Funding AgencyGrant Number
University of Southern California Brain Project (USCBP)UNSPECIFIED
Subject Keywords:Computational modeling; Ontology; Neuroinformatics; Neuroscience databases; BODB
Issue or Number:1
Record Number:CaltechAUTHORS:20140317-102212277
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Official Citation: A Neuroinformatics of Brain Modeling and its Implementation in the Brain Operation Database BODB Michael A. Arbib, Anon Plangprasopchok, James Bonaiuto… Pages 5-26
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:44347
Deposited By: Ruth Sustaita
Deposited On:17 Mar 2014 20:37
Last Modified:03 Oct 2019 06:16

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