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The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs
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DOI：10.1016/j.jmb.2026.169631.png)
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Abstract
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• The CFDE Workbench is a unified web platform developed by the NIH Common Fund Data Ecosystem (CFDE) Data Resource Center (DRC) to integrate metadata and processed data from multiple Common Fund (CF) programs. Such data integration effort facilitates hypothesis generation across CF datasets. • The CFDE Workbench has a Data Portal and an Information Portal. The Data Portal hosts Cross Cut Metadata Model (C2M2) packages, Knowledge Graph (KG) assertions, Set Libraries (XMTs), and attribute tables—to make Common Fund data FAIR (Findable, Accessible, Interoperable, and Reusable) and AI-ready. C2M2 packages contain harmonized metadata mapped to ontologies and dictionaries. • A built-in submission system enables Data Coordination Centers (DCCs) to upload, manage, and assess assets for FAIRness using the FAIRshake toolkit. These assets are listed in the CFDE Workbench Data Matrix consolidating contributions from 18 CF programs. • Uploaded assts are available for cross-program search via an advanced search engine. Additional interactive tools include an AI Assistant that is powered by the Playbook Workflow Builder (PWB), GeneSetCart, CFDE-GSE, and CFDE-KG-UI. These tool facilitate knowledge discovery by combining CF datasets and other relevant resources.
Keywords:
AI-readiness
gene pages
enrichment analysis
knowledge graphs
data management
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