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Ontology integration and experimental metadata in NWB: modeling Patch-seq datasets
Pamela M. Baker, Ryan Ly, Matthew Avaylon, Andrew Tritt, Oliver Ruebel, and Lydia Ng
Presenting author:
Pamela Baker
Neurodata Without Borders (NWB) is a unified data format that provides a comprehensive standard for electrophysiology. Rigorous descriptions of experimental methods are critical for data sharing, including replicating protocols, reproducing data analyses, and driving simulations. As a community standard for data and metadata storage, NWB aims to adhere to the FAIR principles for data sharing. However, lack of metadata standardization results in dataset descriptions that are insufficient to reproduce methods, hinder interoperability of analysis code, and complicate dataset comparison and search. Our goal is to extend the NWB standard to include links to the external resources and persistent identifiers (PIDs) that are a critical component of FAIR datasets.

We have implemented schema extensions to the NWB schema to support the integration of external resources and PIDs and will show how they are used with examples from the Allen Institute for Brain Science’s Patch-seq datasets that include intracellular patch-clamp data in NWB. The metadata areas we targeted are: 1. stimulus metadata describing wave types and parameters that define 1D stimulus waveforms; 2. genotype metadata for storing animal strains, gene loci, alleles and their CRIDs; and 3. spatial location metadata (coordinates, structural annotations, and anatomical terms) from reference atlases. We will also discuss areas for further inclusion of PIDs and controlled terms in NWB.

Funding Acknowledgment: Research reported in this publication was supported by the National Institute of Mental Health of the National Institutes of Health under Award Number R24MH116922 to L. Ng and O. Ruebel.