Carnegie Mellon University researchers have used data mining to create neuroelectro.org, a publicly available website that acts like Wikipedia, indexing the decades worth of physiological data collected about the billions of neurons in the brain.
The site aims to help accelerate the advance of neuroscience research by providing a centralized resource for collecting and comparing this “brain big data.”
A description of the data available and some of the analyses that can be performed using the site are published online by the Journal of Neurophysiology.
The neurons in the brain can be divided into approximately 300 different types based on their physical and functional properties. The data is scattered across tens of thousands of papers in the scientific literature.
“If we want to think about building a brain or re-engineering the brain, we need to know what parts we’re working with,” said Nathan Urban, interim provost and director of Carnegie Mellon’s BrainHub, a global initiative that focuses on how the structure and activity of the brain give rise to complex behaviors. neuroscience initiative.
Shreejoy J. Tripathy, who worked in Urban’s lab when he was a graduate student in the joint Carnegie Mellon/University of Pittsburgh Center for the Neural Basis of Cognition (CNBC) Program in Neural Computation, selected more than 10,000 published papers that contained physiological data describing how neurons responded to various inputs.
He used text mining algorithms to “read” each of the papers. The software found the portions of each paper that identified the type of neuron studied and then isolated the electrophysiological data related to the properties of that neuronal type. It also retrieved information about how each of the experiments in the literature was completed, and corrected the data to account for any differences that might be caused by the format of the experiment. Overall, Tripathy, who is now a postdoc at the University of British Columbia, was able to collect and standardize data for approximately 100 different types of neurons.
Urban and his group validated much of the data, but they also created a mechanism that allows site users to flag data for further evaluation. Users also can contribute new data with minimal intervention from site administrators, similar to Wikipedia.
“It’s a dynamic environment in which people can collect, refine and add data,” said Urban, who is the Dr. Frederick A. Schwertz Distinguished Professor of Life Sciences and a member of the CNBC. “It will be a useful resource to people doing neuroscience research all over the world.”
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