title: Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.
abstract: Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. 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 ofManaged 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. We also introduce the novel concept ofRelationship Attributesfor modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.
authors.affiliation: Computational Research Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Oliver
authors.initials: O
authors.lastname: Rübel
authors.affiliation: Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Max
authors.initials: M
authors.lastname: Dougherty
authors.affiliation: National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.lastname: Prabhat
authors.affiliation: Physical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Denes
authors.affiliation: Neuroscience, University of California, San Francisco Medical Center, University of California, San Francisco San Francisco, CA, USA.
authors.forename: David
authors.initials: D
authors.lastname: Conant
authors.affiliation: Neuroscience, University of California, San Francisco Medical Center, University of California, San Francisco San Francisco, CA, USA.
authors.forename: Edward F
authors.initials: EF
authors.lastname: Chang
authors.affiliation: Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA.
authors.forename: Kristofer
authors.initials: K
authors.lastname: Bouchard
keywords: data format specification; electrophysiology; neuroscience; relationship modeling