Ontology based data structure, Otology of Biological Investigation, OBI, HDF5, OHC, electrophysiology, inner ear, collaboration, data science, voltage clamp
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.
Recommended CitationCitation Information:Farrell, Brenda and Bengtson, Jason, "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" (2019).
DigitalCommons@TMC, Baylor College of Medicine, BCM Research Data. Paper 1.
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
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