BICAN Standards and Documentation

Standards provide a shared framework for organizing and sharing brain cell atlas data. BICAN standards are either adopted from existing standards, or are developed and managed with a governance framework that represent both scientific subject matter experts and infrastructure partners.  Explore the resources below by the four areas: metadata standards, identifiers, data formats, and ontologies.
Metadata
Data Formats
Identifiers
Ontologies
A metadata standard is a set of guidelines or specifications that define how metadata should be structured, formatted, and used within a specific domain. Metadata refers to "data about data," providing information about the content, context, and quality of datasets. BICAN has developed metadata standards for human donors and non-human primates, experimental procedures and cell annotation. All metadata standards developed through BICAN working groups undergo further review by the Metadata and Ontologies working group where they are aligned.
STANDARD (RRID/PID)
BICAN USAGE
DESCRIPTION
BICAN Metadata Standards
doi: 10.5281/zenodo.19377944
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• Developed by BICAN
• Documents metadata schemas
Full suite of BICAN metadata standards hosted in GitHub including human donor, developmental tissue, and non-human primate schemas. This repository also hosts the Allen Institute Taxonomy and Cell Annotation Standards.
Cell Annotation and Taxonomy Standard (CAS)
doi: 10.5281/zenodo.19377944
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• Developed by BICAN
• Used for cell type annotation and taxonomy organization
The cell annotation and taxonomy standard establishes a unified framework for identifying and classifying cell types across datasets. This standard incorporates hierarchical cell type ontologies, marker gene specifications, and confidence metrics for cell type assignments. The schema supports both automated and manual annotation workflows, enabling consistent cell type nomenclature across research groups and experimental platforms.
BICAN Knowledge Base LinkML Schemas
https://github.com/brain-bican/models
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• Developed by BICAN
• Used for BICAN data models
Brain data models in LinkML for the development of the Brain Cell Knowledge Base (BCKB) to ingest and standardize comprehensive cell type information from BICAN's development of a multimodal, multi-species brain cell atlas and disseminate that atlas as an open and interactive community resource for advancing knowledge of the brain
Data standards are specifications or guidelines that define how data should be collected, formatted, and shared. They ensure consistency, accuracy, and interoperability of data across different systems and studies. In biomedical research, data standards are essential for ensuring that data are reliable, comparable, and useful for a wide range of applications.
STANDARD (RRID/PID)
BICAN USAGE
DESCRIPTION
Allen Institute Taxonomy Standard (AIT)
RRID:SCR_027629
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• Documented by BICAN
• Used for cell type taxonomies
Aligned taxonomy format and supporting tools.
Brain Imaging Data Standard (BIDS)
 RRID:SCR_016124
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• Used by BICAN
• MRI data at DANDI
Provides a consistent way to organize neuroimaging data
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• Used by BICAN
• Morphology data at BIL data archive
Text-based (ASCII text) files that describe three-dimensional neuronal or glial morphology. These digital reconstructions represent morphology as a vectorized tree structure, made of a series of connected nodes.
Neurodata Without Borders
(NWB 2.0)
 RRID:SCR_015242
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• Used by BICAN
• Patch-seq electrophysiology data at DANDI
A data standard for neurophysiology to share, archive, use, and build analysis tools for neurophysiology data.
Identifier schemas are structured systems for assigning unique identifiers to entities such as genes, proteins, diseases, and clinical trials. These identifiers are used to ensure that each entity can be uniquely and unambiguously referenced across different databases and systems. In biomedical research, identifier schemas play a crucial role in organizing, accessing, and integrating data.
Standard (RRID/PID)
BICAN Usage
Description
NHash Identifier
 RRID:SCR_025313
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• Used by BICAN
• Issued for NIMP-managed entities
Light-weight, block chain style resource identifiers for tracking research resource linkage, provenance, utilization, and visualization. NHash identifiers incorporate a set of cryptographic hash functions based on N-grams, with combination of additional encryption techniques such as shift cipher.
Research Resource Identifiers
RRID:SCR_015949
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• Used by BICAN
• Issued for major resources
Identifier repository for research resources.
An ontology is a structured framework that represents a set of concepts within a specific domain and the relationships between those concepts. It essentially serves as a formal naming and definition of types, sub-types, and hierarchical relationships. Ontologies are designed to facilitate the sharing and reuse of knowledge by providing a common vocabulary and a well-defined structure.
Standard (RRID/PID)
BICAN Usage
Description
Harmonized Ontology of Mammalian Brain Anatomy  (HOMBA)
RRID:SCR_027628
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• Developed by BICAN
• Used to annotate BICAN tissue, data and cells
Harmonized cross-species taxonomy of 2341 brain and spinal cord structures. Derived from the Allen Developing Human Brain Atlas (DHBA) ontology, the HOMBA is hierarchical, allowing users to aggregate structures from fine grain parcellations to broad regions. Terminology is harmonized across human, primate, and rodent structures with synonymous terms and includes transient developmental structures.
Cell Ontology
RRID:SCR_004251
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• Updated by BICAN to include new cell types
• Includes new BICAN-derived basal ganglia cell types
A reference ontology designed to classify and describe cell types across different organisms. It serves as a resource for model organism and bioinformatics databases.
Ontology of Biomedical Investigations
 RRID:SCR_006266
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• Used by BICAN
• Integrated with LinkML models
An integrated ontology for the description of life-science and clinical investigations
Atlas Ontology Model
 RRID:SCR_023813
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• Used by BICAN
• Packaging of brain common coordinate frameworks
A standardized, machine-readable framework designed to harmonize brain atlases by defining the relationships between four core elements: reference data, coordinate system, annotation set, and terminology