The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs

• 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. The NIH Common Fund Data Ecosystem (CFDE) program was established to facilitate data accessibility and interoperability across multiple Common Fund (CF) programs, promote collaborations and accelerate discoveries by combining diverse data types from different CF programs. The CFDE Data Resource Center (DRC) was tasked with developing two web-based portals: an Information Portal to serve information about the CFDE, and a Data Portal to host harmonized metadata and processed data contributed by participating CF Data Coordination Centers (DCCs) and other sources. To achieve these goals, the CFDE DRC developed the CFDE Workbench, a web-based platform that hosts processed data, metadata, tools, use cases, and analyses developed by the CFDE. The Cross-Cut Metadata Model (C2M2) and several other processed data are hosted by the CFDE Workbench, including set libraries (XMTs), Knowledge Graph (KG) assertions, and attribute tables. These processed data formats make information derived from CF programs more findable, accessible, interoperable, and reusable (FAIR), and artificial intelligence (AI)-ready for cross-DCC knowledge discovery. Besides serving data, metadata, and code assets, the CFDE Workbench has also developed several tools that utilize these resources to enable cross-CF-program knowledge discovery use cases. Overall, the CFDE Workbench is a platform that consolidates efforts toward making CF resources harmonized, FAIR, and AI-ready. The CFDE Workbench website is available from https://cfde.cloud .