BICCN Standards, Best Practices, and Recommendations

As per FAIR, the BICCN seeks to utilize existing standards where they are available, while developing BICCN standards as necessary to fill in the gaps. The BCDC works closely with the BRAIN archives through the Infrastructure Working Group to ensure that standards are harmonized across the consortium where possible. Below are lists of standards and best practices in use in the BICCN.


Metadata and File Formats

 BCDC Metadata Standard for Collections and Samples

High level descriptive metadata to describe BICCN data collections. Instructions and templates for providing information about projects and data collections, and their descriptive metadata which must be submitted for each data collection milestone.  In use by: BCDC for the BICCN Data Catalog.

Project instructions              Data Collection Inventory BICCN Data Catalog

Basic descriptive metadata for samples and specimens profiled in BICCN. Instructions and templates for data submission are provided. An inventory of samples and associated cells or brains profiled for each sample for each dataset, reported on a quarterly basis. This is suitable for identifying the transgenic line and anatomic region sampled in a manageable spreadsheet, but is not intended to include more detailed provenance. In use by: BCDC for the BICCN Data Catalog.

Essential Metadata for 3D Microscopy

Metadata standard for a 3D microscopy dataset to support reuse by scientists who did not generate the data. 3D microscopy data submitted to BIL must adhere to this metadata standard.  In use by: BIL Data Archive.

 

NeuroData Without Borders (NWB2.0)

Data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. In use by: DANDI Archive.  Endorsed by: INCF.

DANDI archive documentation

BIDS-Brain Imaging Data Standard

Data standard for neuroimaging data (e.g., MRI).   In use by: DANDI Archive.  

BIDS-Microscopy:

A proposal extending Brain Imaging Data Structure (BIDS) to 3D Microscopy. 3D microscopy submitted specifically to DANDI archive will adhere to this standard.  In use by: DANDI Archive.   

SWC morphology format

Open data format for encoding neuro morphologies.  Required for morphological data submitted to BIL and NeuroMorpho.org.  NeuroMorpho.org uses the tool L-Measure to convert common formats into SWC. In use by:  BIL Data Archive, Neuromorpho.org.

NeuroMorpho documentation on use of SWC
Discussion on SWC at the NEURON forum

Spatial and Semantic Standards

 

BCDC Metadata Standard for Collections and Samples

High level descriptive metadata to describe BICCN data collections. Instructions and templates for providing information about projects and data collections, and their descriptive metadata which must be submitted for each data collection milestone.  In use by: BCDC for the BICCN Data Catalog.

Basic descriptive metadata for samples and specimens profiled in BICCN. Instructions and templates for data submission are provided. An inventory of samples and associated cells or brains profiled for each sample for each dataset, reported on a quarterly basis. This is suitable for identifying the transgenic line and anatomic region sampled in a manageable spreadsheet, but is not intended to include more detailed provenance. In use by: BCDC for the BICCN Data Catalog.

Essential Metadata for 3D Microscopy

Metadata standard for a 3D microscopy dataset to support reuse by scientists who did not generate the data. 3D microscopy data submitted to BIL must adhere to this metadata standard.  In use by: BIL Data Archive.

 

 

NeuroData Without Borders (NWB2.0)

Data standard for neurophysiology, providing neuroscientists with a common standard to share, archive, use, and build common analysis tools for neurophysiology data. In use by: DANDI Archive.  Endorsed by: INCF.

DANDI archive documentation

 

BIDS-Brain Imaging Data Standard

Data standard for neuroimaging data (e.g., MRI).   In use by: DANDI Archive.  

 

BIDS-Microscopy:

A proposal extending Brain Imaging Data Structure (BIDS) to 3D Microscopy. 3D microscopy submitted specifically to DANDI archive will adhere to this standard.  In use by: DANDI Archive.   

 

SWC morphology format

Open data format for encoding neuro morphologies.  Required for morphological data submitted to BIL and NeuroMorpho.org.  NeuroMorpho.org uses the tool L-Measure to convert common formats into SWC. In use by:  BIL Data Archive, Neuromorpho.org.
NeuroMorpho documentation on use of SWC
Discussion on SWC at the NEURON forum

 


Identifiers and Protocols

   

ORCID

ORCIDs are unique identifiers for researchers.  All investigators should provide ORCIDs for contributors to datasets to facilitate cross-dataset linkage and to receive credit for publishing datasets.

Orcid.org website

See documentation at individual archives for adding ORCIDs.

Research Resource Identifiers (RRIDs)

Unique identifier for antibodies, digital tools, cell lines, organisms, plasmids and biosamples. If you create a new tool for BICCN, please obtain an RRID.  In use by: BICCN Data Catalog, BICCN.org, journals and publications.

RRID portal

Introduction to RRIDs

 

Protocols.io

BICCN investigators are required to share experimental protocols. Protocols.io is one option for this that provides a DOI and version history for protocols.  In use by: BICCN members, BICCN Data Catalog

BICCN protocols.io group