Brain Cell Atlas: From Data to Knowledge Base

Presenter

Yong Yao, Ph.D.
Division of Neuroscience and Basic Behavioral Science

Goal

The goal of this concept is to continue supporting an integrated BRAIN® Initiative Cell Atlas Network (BICAN) Coordinating Unit for Biostatistics, Informatics, and Engagement (CUBIE) that will (i) enable the exploration of large-scale brain cell atlas data and knowledge, (ii) inspire research in brain function and disorders, and (iii) ensure research rigor and data reproducibility by making the data Findable, Accessible, Interoperable, and Reusable (FAIR). This will provide the foundation for a knowledge base with consensus brain cell taxonomies, ontologies, and community data standards.

Rationale

The BRAIN Initiative 2.0 Advisory Committee to the NIH Director recommended that NIH “generate a comprehensive cell-type atlas in the human brain” and “establish a data ecosystem for cell types allowing the integration of different facets of neuronal phenotype.” Rich multimodal brain cell molecular, anatomical, and physiological data have been generated by the BRAIN Initiative Cell Census and Atlas Networks (BICCN, BICAN) since the inception in 2014. This data remains to be fully integrated to generate new insights into brain function and disease. While the current data coordination and integration activities are supported by BICAN through 2027, additional large volumes of data will be generated by the BRAIN Initiative consortia and the broader research community in the years to come. One of the strategic goals of the BRAIN Initiative is to develop an overarching BRAIN Data Commons that encompasses federated domain-specific data archives and knowledge bases to bring together these multimodal datasets to enable discovery and hypothesis-driven research by the scientific community.

As the first step toward a unified Data Commons, the BRAIN Initiative proposes to continue supporting an integrated CUBIE program that will:

• Develop and operate common data processing pipelines and implement brain cell atlas data standards to facilitate brain cell annotation and knowledge derivation.
• Provide a systematic governance structure and technical support to coordinate and collaborate with community brain data platforms (e.g., data archives, brain disease consortia, brain resources) to facilitate the implementation of best practices and standards and data integration.
• Provide the foundation to create a comprehensive, high quality and reliable Brain Cell Atlas Knowledge Base that:
  • establishes reference brain cell taxonomies and spatially resolved brain cell atlases,
  • adopts reliable artificial intelligence/machine learning models to accelerate discovery and facilitate hypothesis generation, and
  • provides an interactive and dynamic information system and web interface for information querying, data mapping, user feedback, and future expansion and integration with other domain knowledge bases.

Overall, continuing to support CUBIE is critical to address the challenges and opportunities in the analyses and integration of the vast amounts of brain cell atlas data and to develop a comprehensive brain cell knowledge base.