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

Evangelista, J. E.; Clarke, D. J. B.; Xie, Z.; Olaiya, S.; Kim, H.; Marino, G. B.; Byrd, A. I.; Srinivasan, S.; Maurya, M. R.; Jenkins, S. L.; Lutsky, A. D.; Sasaya, L.; Lachmann, A.; Ahmed, N.; Diamant, I.; Sanchez, E.; Ramachandran, S.; Subramaniam, S.; Ma'ayan, A.

doi:10.1101/2025.02.04.636535

bioRxiv · 10.1101/2025.02.04.636535

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

Evangelista, J. E.·Clarke, D. J. B.·Xie, Z.·Olaiya, S.·Kim, H.·Marino, G. B.·Byrd, A. I.·Srinivasan, S.·Maurya, M. R.·Jenkins, S. L.·Lutsky, A. D.·Sasaya, L.·Lachmann, A.·Ahmed, N.·Diamant, I.·Sanchez, E.·Ramachandran, S.·Subramaniam, S.·Ma'ayan, A.

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Abstract

The NIH Common Fund Data Ecosystem (CFDE) program was established to facilitate data accessibility and interoperability across multiple Common Fund (CF) programs and promote collaborations and new discoveries by combining data 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 highly processed data, metadata, tools, use cases, and analyses developed by the CFDE. The Crosscut Metadata Model (C2M2) and several other processed data formats 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. In addition to these processed data formats, several other assets are served by the Workbench, including Extract Transform Load (ETL) pipelines, OpenAPI-documented and SmartAPI-registered Representational State Transfer (REST) Application Programming Interfaces (APIs), entity pages such as gene, drug, disease, or tissue landing pages, Playbook Workflow Builder (PWB) metanodes which are codified workflow steps involving DCC APIs, and chatbot specifications which are prompts helping chatbots to use DCC APIs to answer a wide range of user queries. Besides serving data, metadata, and code assets, the CFDE Workbench also has several tools that use these data, metadata, and code assets to enable cross-CF-program knowledge discovery use cases. Overall, the CFDE Workbench is a platform that consolidates efforts toward making CF programs funded resources harmonized, FAIR, and AI-ready. The CFDE Workbench website is available from: https://cfde.info/.

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Evangelista, J. E., Clarke, D. J. B., Xie, Z., Olaiya, S., Kim, H., Marino, G. B., Byrd, A. I., Srinivasan, S., Maurya, M. R., Jenkins, S. L., Lutsky, A. D., Sasaya, L., Lachmann, A., Ahmed, N., Diamant, I., Sanchez, E., Ramachandran, S., Subramaniam, S., Ma'ayan, A.. 2025-02-05. The CFDE Workbench: Integrating Metadata and Processed Data from Common Fund Programs. https://doi.org/10.1101/2025.02.04.636535

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