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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.
Sample instructions
Sample Inventory
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.

Brain Image Library
Data model  
 

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.
NWB help pages
DANDI archive documentation
INCF Standards and Best Practices Portfolio

BIDS-Brain Imaging Data Standard

Data standard for neuroimaging data (e.g., MRI).   In use by: DANDI Archive.  
DANDI archive standards
BIDS starter kit wiki

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.   
DANDI archive standards
BIDS Microscopy Extension

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

 

Allen Common Coordinate Framework v3

The Allen Mouse Common Coordinate Framework (CCF)   is the main anatomic data browser and coordinate environment for mouse data within the BICCN. If you are acquiring spatial data in the mouse, it should be registered to the CCF V3. Registered data is available through BIL data archive. Anatomic terms associated with the this CCF are used as annotations of samples and specimens. In use by: BCDC for the BICCN Data Catalog.

Description

List of tools for registering images.  

Templates for registering different data types.

Link to atlas viewer

Allen Human Atlas - 3D

The Allen Human Atlas - 3D is a is a parcellation of the non-linear average of the MNI152 using the same anatomical ontology as the section based Allen Human Reference Atlas. If you are acquiring samples in the human, approximate location of the sample should be registered to the Allen Human Atlas - 3D. In use by: BCDC for the BICCN Data Catalog.

Introduction to the Allen Human Atlas 3D

 

EStim Ontology

Ontology for describing electrophysiology stimulation parameters, developed by an INCF cross project working group. This ontology is suitable for use in NWB formats. 

DANDI archive standards

BIDS starter kit wiki

UBERON multispecies ontology

Ontology for multi-species anatomical terms. All anatomical metadata should be mapped to UBERON identifiers or a particular atlas. A mapping between the Allen Brain Atlas has been completed.  If the latter, the full reference for the atlas should be supplied.

 

DANDI archive standards

BIDS starter kit wiki

Neuroscience methods ontology

Covers major neuroscience techniques.  Based on NIFSTD methods ontology, OBI and EFO.   Use this ontology to map techniques, modalities, assays, devices and tools to a controlled vocabulary. In use by: BCDC for the BICCN Data Catalog, BIL, NeMO

Instructions on working with and adding a term can be found here.

 

Brain Data Standards Ontology

Ontology for representing data-defined cell types (omics) from the BICCN flagship paper. Used by BRAIN Data Standards group for -omics defined cell types. In use by: BICCN Mouse Primary Cortex Mini-Atlas – Cell Types Explorer.

 

Github repo

 

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