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Updated: Jan 13, 2026

An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome
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The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs.

John Erol Evangelista1, Daniel J B Clarke1, Anna I Byrd1

  • 1Department of Pharmacological Sciences, Windreich Department of Artificial Intelligence and Human Health, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA.

Journal of Molecular Biology
|January 8, 2026
PubMed
Summary
This summary is machine-generated.

The NIH Common Fund Data Ecosystem (CFDE) Workbench harmonizes data, making it FAIR and AI-ready. This platform enhances data accessibility and interoperability for accelerated scientific discovery across programs.

Keywords:
AI-readinessdata managementenrichment analysisgene pagesknowledge graphs

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Area of Science:

  • Biomedical Informatics
  • Data Science
  • Genomics

Background:

  • The NIH Common Fund (CF) program aims to improve data accessibility and interoperability.
  • Diverse data types from CF programs require harmonization for collaborative research.
  • The CFDE Data Resource Center (DRC) was established to manage CF data.

Purpose of the Study:

  • To develop web-based portals for information and data access.
  • To create a platform for hosting harmonized metadata and processed data.
  • To facilitate cross-program knowledge discovery and accelerate research.

Main Methods:

  • Development of the CFDE Workbench, a web-based platform.
  • Hosting of processed data, metadata, and tools.
  • Implementation of the Cross-Cut Metadata Model (C2M2) and other data formats (XMTs, KG assertions).

Main Results:

  • The CFDE Workbench hosts harmonized metadata and processed data.
  • Data formats are FAIR (Findable, Accessible, Interoperable, Reusable) and AI-ready.
  • Tools and use cases for cross-program knowledge discovery are available.

Conclusions:

  • The CFDE Workbench consolidates efforts to make CF resources harmonized, FAIR, and AI-ready.
  • The platform supports accelerated scientific discovery by enhancing data accessibility and interoperability.
  • The CFDE Workbench promotes collaboration and efficient data utilization.