The AnDO project: a repository for tools related to the BIDS-animal-ephys Extension Proposal (BEP032)

April 2021

The Animal Data Organization (AnDO) is a project initiated at the Institut de Neurosciences de la Timone, in Marseille, France, in order to set up a standardization of the experimental data recorded in animal models. Since its launch in early 2020, its aims have significantly evolved following these axes:

• first, we have opened our desire for standardization to the community through the launch of a Working Group endorsed by the INCF; please feel free to join the group to participate in this effort: https://www.incf.org/sig/incf-working-group-standardized-data ; we are meeting approximately every two months and we are making progress in subgroups on well defined issues between each meeting;

• second, after discussions within the group, we have initiated a specific standardization effort for electrophysiology, as a BIDS Extension Proposal (BEP032: https://bids.neuroimaging.io/get_involved.html ); we are actively looking for feedback from the community on this proposal, so feel free to directly comment in the document that details the data and metadata organization: http://bit.ly/BIDS-animal-ephys.

At this moment, this repository provides several tools, amongst them a validator (the AnDOChecker) and generator functions for user-friendly setup of an AnDO structure. The validator complies with the latest specifications described in the BEP032 document. Please note that this validator is a temporary tool and to be used until BEP032 is officially included in BIDS. From then on the official BIDS validator will replace the AnDOChecker. We are committed to keeping the AnDO tools up to date to follow the latest modifications of the BEP032 that will occur to cope with the feedback from the community.

Example datasets

Here is a summarized view of an electrophysiology dataset that follows the proposed organization.

Real examples of datasets that are organized following the BEP032 rules are available on this repository: https://gin.g-node.org/NeuralEnsemble/BEP032-examples

Available tools

AnDOChecker:

• Checks the validity of a dataset with respect to the BIDS-animal-ephys BEP specifications. The specifications that define what is checked by this function is available in the following document: http://bit.ly/BIDS-animal-ephys

AnDOGenerator:

• Generates a BIDS-animal-ephys folder structure that follows the BEP03 specifications with a overview CSV files and optional metadata files as input.

---

Indices and tables

• Index

• Module Index

• Search Page