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An extensible brain knowledge base and toolset spanning modalities for multi-species data-driven cell types

Award Number: U24MH130918
ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/01/2022
PERIOD OF PERFORMANCE END DATE: 06/30/2027

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An extensible brain knowledge base and toolset spanning modalities for multi-species data-driven cell types - Project Summary BRAIN Initiative Cell Census Network (BICCN) is completing a comprehensive cell census of the adult mouse brain, and BRAIN Initiative Cell Atlas Network (BICAN) will extend this work with emphasis on human and non- human primates. Effectively organizing, summarizing, accessing, and refining these atlases is critical to maximizing their impact on science. This proposal is to develop an extensible 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. The BCKB will be initialized during this project with multi- dimensional brain cell type classifications from BICCN and will expand as data and knowledge are produced by BICAN researchers. Under Aim 1, we will create an adaptive knowledge graph for linking brain cell information. Spatial aggregation will be done using common coordinate frameworks. A flexible graph-based data model will capture discrete and continuous cell type relationships. The work will start with cross-species MOp data and comprehensive whole- brain mouse datasets from BICCN and later extend into BICAN’s whole-brain molecular and spatial transcriptomics data in human and non-human primates as such data becomes available. Anchoring of taxonomies in single cell molecular and spatial transcriptomics provides a robust framework for integrating multimodal data that is spatially mapped and/or cell types mapped. An ecosystem of tools for curating, annotating, mapping, and visualization of cell type data will be created in Aim 2. We will build and extend tools, such as the initial Cell Types Cards showcasing BICCN’s MOp results, so BICAN teams and public labs can share and refine brain cell type taxonomies and anatomical integration. The tools framework developed for this aim will provide a central hub, akin to an “app store,” to access our tools and others from the community to interact with cell type data. This connected tools framework will streamline scientific workflows and encourage FAIR practices. As part of Aim 3, we will develop an infrastructure to link brain cell data and knowledge. This infrastructure will enable ingesting, storing, searching, and curating neuroscientific information from multiple sources into a linked information platform. This knowledge infrastructure will help connect disparate pieces of cell type information using expert annotations, machine-learning inferences, and derivations using provenance mechanisms. We will use Allen Institute’s Brain Knowledge Platform for initial implementation. Finally, in Aim 4 we will gather, curate, and integrate information and knowledge from BICAN teams by conducting annual hands- on training and feedback workshops. These events will create engagement within and outside BICAN projects and foster community-based evolution, sustainability, and governance.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $0 )
2026	2025	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	001	4	7/2/2026	NON-COMPETING CONTINUATION	$0
2026	2025	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	000	4	1/29/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2025 ( Subtotal = $1,921,187 )
2025	2025	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	000	4	6/17/2025	NON-COMPETING CONTINUATION	$1,921,187
														Subtotal = $1,921,187

Issue Date FY: 2024 ( Subtotal = $1,914,560 )
2024	2024	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	001	3	6/20/2024	NON-COMPETING CONTINUATION	$1,914,560
2024	2023	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	000	2	4/5/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $1,914,560

Issue Date FY: 2023 ( Subtotal = $2,134,652 )
2023	2023	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	000	2	6/26/2023	NON-COMPETING CONTINUATION	$2,134,652
														Subtotal = $2,134,652

Issue Date FY: 2022 ( Subtotal = $2,096,841 )
2022	2022	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Mental Health Research Grants	000	1	8/19/2022	NEW	$2,096,841
														Subtotal = $2,096,841

Grand Total All Awards = $8,067,240

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An extensible brain knowledge base and toolset spanning modalities for multi-species data-driven cell types

Award Number: U24MH130918

ORGANIZATION: NATIONAL INSTITUTE OF MENTAL HEALTH

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 09/01/2022

PERIOD OF PERFORMANCE END DATE: 06/30/2027

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