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About ear-1

Information about the ear-1 data set.

Summary

This data collection describes the electrical properties of outer hair cells isolated from the mammalian cochlea of the domestic guinea pig. This data was obtained by performing whole-cell patch clamp voltage clamp assay on cells and monitoring the electrical admittance during a DC voltage ramp. The membrane capacitance was then calculated at each membrane potential from this admittance, and the voltage-independent and voltage-dependent membrane capacitance was determined upon further analysis. In some case the DC conductance was also measured by interrogation of the cell with voltage-step function which was calculated from the change in the mean steady-state current with respect to DC voltage. The data collection contains results from 89 cells isolated from the domestic guinea pig.

This data was originally stored in MATLAB in an unstructured format. Each recording form a cell was described by 82 fields with the struct format and the collection was stored as an array of structures. This data has now been curated by a collaboration between the scientist and data architect and is now described with a variant of the Ontology of Biological Investigation (OBI) coined OBI based Inner Ear Electrophysiology (OBI_IEE)). The data has been transformed to the non-proprietary format: Hierarchical Data Format version 5 (HDF5) format where this application ontology was mirrored to provide the metadata and nested data architecture within HDF5. Each digital specimen is displayed in a tree configuration (like directories in a computer) and consists of six main branches based on the ontology classes. The curation and archiving of the data set is described in

  1. Farrell B, Bengtson J. Ontology based data architecture to promote data sharing in electrophysiology. In: P. Jaiswal LC, M. A. Haendel, C. J. Mungall editor. Proceedings of the 9th International Conference on Biological Ontology (ICBO); August 7-10, 2018; Corvallis, Oregon, USA2018. http://ceur-ws.org/Vol-2285/
  2. Farrell B, Bengtson J (2019) Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. PLoS ONE 14(10): e0223984. https://doi.org/10.1371/journal.pone.0223984

The experimental methods and results are described in

  1. Corbitt C, Farinelli F, Brownell WE, Farrell B. Tonotopic relationships reveal the charge density varies along the lateral wall of outer hair cells. Biophys J. 2012 2012/06/20/;102(12):2715-24. PubMed PMID: 22735521.
  2. Farrell, B. B.S. Skidmore, V. Rajesekharan and W. E. Brownell. A novel theoretical framework reveals more than one voltage-sensing pathway in the lateral membrane of outer hair cells. Journal of General Physiology 6 July 2020; Volume 152 Number 7. https://doi.org/10.1085/jgp.201912447.

Format of the data

The data are stored in hdf5 and Matlab along with an OWL file which describes the application ontology.  Matlab scripts to analyze the data and to convert the data from hdf5 to Mat file format and back are provided.  Details are given in the data description document listed at the bottom of this page.  Total data size is about 98 MB.

Conditions for using the data

The data is made available under a Creative Commons Zero license (CC0). If you publish any work using the data, please cite the publications provided above also cite the data collection using the following:

Farrell, B and J. Bengtson (2019); Data collection curated with an application ontology describes the methods and results upon performing an ex-vivo voltage-clamp assay on outer hair cells of the mammalian cochlea. CRCNS.org
http://dx.doi.org/10.6080/K0571975

The above citation uses a Digital Object Identifier (DOI) which is assigned to the data set.  The DOI was created using DataCite (www.datacite.org) and the California Digital Library, "EZID" system (n2t.net/ezid/).

How to download the data

The data may be downloaded from:
https://portal.nersc.gov/project/crcns/download/ear-1
Using a CRCNS.org account.  See the download link for more information about downloading.

Getting help using the data.

If you have questions about using the data, post them on the forum for using data sets.

Documentation files

crcns_ear-1_data_description.pdf

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