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.

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 and J. Bengtson. 2019. Scientist and data architect collaborate to curate and archive an inner ear electrophysiology data collection. Submitted for publication
The experimental methods and results are described in
3.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.
4.Paper that describe some new scientific findings from this data collection are being submitted concurrently with paper number (2) above.