NCI Cancer Research Data Commons: Core Standards and Services

Brady, Arthur; Charbonneau, Amanda; Grossman, Robert L.; Creasy, Heather H.; Renner, Robinette; Pihl, Todd; Otridge, John; Kim, Erika; ,; Barnholtz-Sloan, Jill S.; Kerlavage, Anthony R.

doi:10.1158/0008-5472.can-23-2655

Cancer Research

2024

DOI: 10.1158/0008-5472.can-23-2655

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NCI Cancer Research Data Commons: Core Standards and Services

Arthur Brady,

Amanda Charbonneau,

Robert L. Grossman

et al.

Abstract: The National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) is a collection of data commons, analysis platforms, and tools that make existing cancer data more findable and accessible by the cancer research community. In practice, the two biggest hurdles to finding and using data for discovery are the wide variety of models and ontologies used to describe data, and the dispersed storage of that data. Here, we outline core CRDC services to aggregate descriptive information from multiple studies for f… Show more

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Cited by 3 publications

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NCI Cancer Research Data Commons: Lessons Learned and Future State

Kim,

Davidsen,

Davis-Dusenbery

et al. 2024

Cancer Research

Self Cite

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More than ever, scientific progress in cancer research hinges on our ability to combine datasets and extract meaningful interpretations to better understand diseases and ultimately inform the development of better treatments and diagnostic tools. To enable the successful sharing and use of big data, the NCI developed the Cancer Research Data Commons (CRDC), providing access to a large, comprehensive, and expanding collection of cancer data. The CRDC is a cloud-based data science infrastructure that eliminates the need for researchers to download and store large-scale datasets by allowing them to perform analysis where data resides. Over the past 10 years, the CRDC has made significant progress in providing access to data and tools along with training and outreach to support the cancer research community. In this review, we provide an overview of the history and the impact of the CRDC to date, lessons learned, and future plans to further promote data sharing, accessibility, interoperability, and reuse.

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NCI Cancer Research Data Commons: Lessons Learned and Future State

Kim,

Davidsen,

Davis-Dusenbery

et al. 2024

Cancer Research

Self Cite

View full text Add to dashboard Cite

show abstract

NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data

Thangudu,

Holck,

Singhal

et al. 2024

Cancer Research Communications

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Proteomics has emerged as a powerful tool for studying cancer biology, developing diagnostics, and therapies. With the continuous improvement and widespread availability of high-throughput proteomic technologies, the generation of large-scale proteomic data has become more common in cancer research, and there is a growing need for resources that support the sharing and integration of multi-omics datasets. Such datasets require extensive metadata including clinical, biospecimen, and experimental and workflow annotations that are crucial for data interpretation and reanalysis. The need to integrate, analyze, and share these data has led to the development of NCI’s Proteomic Data Commons (PDC), accessible at https://pdc.cancer.gov. As a specialized repository within the NCI Cancer Research Data Commons (CRDC), PDC enables researchers to locate and analyze proteomic data from various cancer types and connect with genomic and imaging data available for the same samples in other CRDC nodes. Presently, PDC houses annotated data from more than 160 datasets across 19 cancer types, generated by several large-scale cancer research programs with cohort sizes exceeding 100 samples (tumor and associated normal when available). In this article, we review the current state of PDC in cancer research, discuss the opportunities and challenges associated with data sharing in proteomics, and propose future directions for the resource. Significance: The Proteomic Data Commons (PDC) plays a crucial role in advancing cancer research by providing a centralized repository of high-quality cancer proteomic data, enriched with extensive clinical annotations. By integrating and cross-referencing with complementary genomic and imaging data, the PDC facilitates multi-omics analyses, driving comprehensive insights, and accelerating discoveries across various cancer types.

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Usage of the National Cancer Institute Cancer Research Data Commons by Researchers: A Scoping Review of the Literature

Chen,

Kim,

Davidsen

et al. 2024

JCO Clin Cancer Inform

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PURPOSE Over the past decade, significant surges in cancer data of all types have happened. To promote sharing and use of these rich data, the National Cancer Institute's Cancer Research Data Commons (CRDC) was developed as a cloud-based infrastructure that provides a large, comprehensive, and expanding collection of cancer data with tools for analysis. We conducted this scoping review of articles to provide an overview of how CRDC resources are being used by cancer researchers. METHODS A thorough literature search was conducted to identify all relevant publications. We included publications that directly cited CRDC resources to specifically examine the impact and contributions of CRDC by itself. We summarized the distributions and trends of how CRDC components were used by the research community and discussed current research gaps and future opportunities. RESULTS In terms of CRDC resources used by the research community, encouraging trends in utilization were observed, suggesting that CRDC has become an important building block for fostering a wide range of cancer research. We also noted a few areas where current applications are rather lacking and provided insights on how improvements can be made by CRDC and research community. CONCLUSION CRDC, as the foundation of a National Cancer Data Ecosystem, will continue empowering the research community to effectively leverage cancer-related data, uncover novel strategies, and address the needs of patients with cancer, ultimately combatting this disease more effectively.

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NCI Cancer Research Data Commons: Core Standards and Services

Cited by 3 publications

References 14 publications

NCI Cancer Research Data Commons: Lessons Learned and Future State

NCI Cancer Research Data Commons: Lessons Learned and Future State

NCI’s Proteomic Data Commons: A Cloud-Based Proteomics Repository Empowering Comprehensive Cancer Analysis through Cross-Referencing with Genomic and Imaging Data

Usage of the National Cancer Institute Cancer Research Data Commons by Researchers: A Scoping Review of the Literature

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