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BRAINformat: A Data Standardization Framework for Neuroscience Data

Oliver Rübel, Prabhat, Peter Denes, David Conant, Edward Chang, Kristofer Bouchard
doi: https://doi.org/10.1101/024521
Oliver Rübel
1Computational Research Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, USA
2National Energy Research Scientific Computing Center, LBNL, Berkeley, CA, USA
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  • For correspondence: oruebel@lbl.gov
Prabhat
2National Energy Research Scientific Computing Center, LBNL, Berkeley, CA, USA
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Peter Denes
3Physical Sciences Division, LBNL, Berkeley, CA, USA
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David Conant
4UCSF Medical Center, University of California San Francisco, San Francisco, CA, USA
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Edward Chang
4UCSF Medical Center, University of California San Francisco, San Francisco, CA, USA
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Kristofer Bouchard
5Biological Systems and Engineering Division, LBNL, CA, USA
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ABSTRACT

Neuroscience is entering the era of ‘extreme data’ with little experience and few plans for the associated volume, velocity, variety, and veracity challenges. This is a serious impediment for both the sharing of data across labs, as well as the utilization of modern and high-performance computing capabilities to enable data driven discovery. Here, we introduce BRAINformat, a novel file format and model for management and storage of neuroscience data. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data.

We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. The BRAINformat is built off of HDF5, enabling portable, scalable, and self-describing data storage. We introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects, and discuss the annotation of data using dedicated data annotation modules provided by the BRAINformat library. Based on these concepts we implement dedicated, application-oriented modules and design a data standard for neuroscience data. The BRAINformat software library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted August 13, 2015.
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BRAINformat: A Data Standardization Framework for Neuroscience Data
Oliver Rübel, Prabhat, Peter Denes, David Conant, Edward Chang, Kristofer Bouchard
bioRxiv 024521; doi: https://doi.org/10.1101/024521
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BRAINformat: A Data Standardization Framework for Neuroscience Data
Oliver Rübel, Prabhat, Peter Denes, David Conant, Edward Chang, Kristofer Bouchard
bioRxiv 024521; doi: https://doi.org/10.1101/024521

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