The UrbanLegend Project: a system for cellular neurophysiology data management and exploration
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1
University of British Columbia, Centre for High Throughput Biology, Canada
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2
Elsevier, Elsevier Research Data Services, Netherlands
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3
Carnegie Mellon University, Biology, United States
A challenge in neuroinformatics is translating developed tools like standards, best practices, and ontologies to experimental laboratories. While experimentalists generally agree that such standards are useful and can potentially help mitigate issues of scientific reproducibility, integrating these tools into scientists’ existing workflows has been difficult. Using the example of cellular neurophysiology, experimentalists use a combination of technologies for acquiring and storing electrophysiological data including custom acquisition software (e.g., IGORPro or AxoClamp) and pen-and-paper lab notebooks to store relevant methodological details. While these laboratory-specific workflows are quite effective within each lab, the heterogeneous nature of how these data are stored and annotated makes within- and cross-lab data compilation extremely difficult. Here, we describe the UrbanLegend Project, a collaboration between the lab of Nathan Urban at Carnegie Mellon University and Elsevier Research Data Services (http://researchdata.elsevier.com), designed to improve in-lab practices of neurophysiological data annotation and standardization.
The UrbanLegend project is composed of the following primary components (schematic in Figure 1): 1) a web-based electronic lab notebook application for annotating in vitro electrophysiological recordings with essential methodological details; and 2) a data browser for visualizing and performing metadata-based searches of recorded data and analyses. Using the lab notebook app while performing an experiment, electrophysiologists enter details like the animal strain used or the neuron type recorded via a series of drop-down menus. This structured data entry approach allows enforcing a common metadata format and the usage of INCF standards and terminologies. Following experiment completion, the collected metadata is uploaded to a relational database and combined with the acquired electrophysiology data files into a semantically-enriched, reusable format for creative data exploration. Specifically, the web-based “Data Dashboard” allows for finding and sorting experiments using metadata as a search filter (e.g., find experiments with animals of age P10-12 and where olfactory bulb mitral or granule cells were recorded). Additionally, the dashboard facilitates interactive visualization of the collected sweeps as well as simple analyses.
While the UrbanLegend Project is currently implemented within the Urban Lab, we are actively seeking to scale-up its utilization to additional in vitro neurophysiology labs at Carnegie Mellon and beyond. We hope that by improving data organization, archiving, and sharing practices, our system will show clear benefits to the scientists performing and analyzing research data and ultimately empower demonstrably better neuroscience research.
Acknowledgements
This work was funded by the NIDCD (R01DC0005798) and Elsevier Research Data Services.
Keywords:
neuron electrophysiology,
digital lab notebook,
data sharing,
experimental metadata,
Reproducible Research,
data visualization,
neuroscience infrastructure
Conference:
Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014.
Presentation Type:
Demo, not to be considered for oral presentation
Topic:
General neuroinformatics
Citation:
Tripathy
SJ,
Alder
J,
Burton
SD,
Harviston
M,
Marques
D,
Urban
NN and
De Waard
A
(2014). The UrbanLegend Project: a system for cellular neurophysiology data management and exploration.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2014.
doi: 10.3389/conf.fninf.2014.18.00077
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Received:
28 Apr 2014;
Published Online:
04 Jun 2014.
*
Correspondence:
Dr. Shreejoy J Tripathy, University of British Columbia, Centre for High Throughput Biology, Vancouver, Canada, shreejoy.tripathy@utoronto.ca