NeuroElectro: A window to the world's neuron electrophysiology data

Shreejoy J. Tripathy, Judith Savitskaya, Shawn D. Burton, Nathaniel N. Urban, Richard Gerkin

Research output: Contribution to journalArticlepeer-review

45 Scopus citations

Abstract

The behavior of neural circuits is determined largely by the electrophysiological properties of the neurons they contain. Understanding the relationships of these properties requires the ability to first identify and catalog each property. However, information about such properties is largely locked away in decades of closed-access journal articles with heterogeneous conventions for reporting results, making it difficult to utilize the underlying data. We solve this problem through the NeuroElectro project: a Python library, RESTful API, and web application (at http://neuroelectro.org) for the extraction, visualization, and summarization of published data on neurons' electrophysiological properties. Information is organized both by neuron type (using neuron definitions provided by NeuroLex) and by electrophysiological property (using a newly developed ontology). We describe the techniques and challenges associated with the automated extraction of tabular electrophysiological data and methodological metadata from journal articles. We further discuss strategies for how to best combine, normalize and organize data across these heterogeneous sources. NeuroElectro is a valuable resource for experimental physiologists attempting to supplement their own data, for computational modelers looking to constrain their model parameters, and for theoreticians searching for undiscovered relationships among neurons and their properties.

Original languageEnglish (US)
Article number40
JournalFrontiers in Neuroinformatics
Volume8
Issue numberAPR
DOIs
StatePublished - Apr 29 2014

Keywords

  • API
  • Database
  • Electrophysiology
  • Machine learning
  • Metadata
  • Natural language processing
  • Neuroinformatics
  • Text-mining

ASJC Scopus subject areas

  • Neuroscience (miscellaneous)
  • Biomedical Engineering
  • Computer Science Applications

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