Publication Date

2019

Keywords

Ontology based data structure, Otology of Biological Investigation, OBI, HDF5, OHC, electrophysiology, inner ear, collaboration, data science, voltage clamp

Abstract

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.

This data was originally stored in MATLAB in an unstructured format. This data has now been curated by a collaboration between the scientist (BF) and data architect (JB), 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 data collection contains six main items: (1) the original unstructured data in MATLAB; (2) the data files translated to HDF5 with metadata; (3) MATLAB scripts that facilitate the translation of the data from MATLAB to HDF5; (4) MATLAB scripts that facilitate the translation of the data back to MATLAB from HDF5; (5) MATLAB scripts used to analyze the data and (6) the OWL file describing the variant or application ontology OBI based Inner Ear Electrophysiology (OBI_IEE). The package contains 114 files.

Comments

Papers published where curation and archiving are described

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/.

Paper submitted that describe the curation and archiving of the data

Farrell, B and J. Bengtson. 2019. Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. Submitted for publication

Papers published where the scientific findings from the this data are described

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.

Paper that describe some new scientific findings from this data collection are being submitted concurrently with 2nd curation paper mentioned above.

GitHub site also contains the scripts and OWL file with further details found in README.md.

The site’s URL is https://github.com/gaviganet/OHC_curation

HDF5 Data.zip (44955 kB)
Data stored in HDF5

Original Data.zip (48946 kB)
Original data within MATLAB

OBI_IEE.owl (6275 kB)
OWL file with application ontology

M2HDF5.zip (27 kB)
Scripts that convert data to HDF5

HDF52M.zip (4 kB)
Scripts that convert HDF5 files back to MATLAB

Analysis.zip (8 kB)
Scripts used to analyze data

Share

COinS