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A User-friendly and Powerful R Analysis of Large-scale Datasets
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Datagraphy: toward a systematic approach to dataset discovery.

Pascal Petit1, Nicolas Vuillerme1,2

  • 1Univ. Grenoble Alpes, AGEIS, 38000 Grenoble, France.

Gigascience
|October 22, 2025
PubMed
Summary

Datagraphy offers a structured method for finding and evaluating datasets, improving research transparency and reproducibility. This approach formalizes dataset search, addressing challenges in the big data ecosystem for more efficient data reuse.

Keywords:
big datadata reusedatagraphic searchdatagraphydataset discoveryexposomeinformationopen dataopen scienceresearch practice

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Area of Science:

  • Data Science
  • Research Methodology
  • Information Science

Background:

  • Scientific discovery increasingly relies on data, yet reusing existing datasets is hindered by fragmentation and heterogeneity.
  • Current dataset discovery methods lack standardization, leading to inefficiencies and potential bias.
  • There's a need for a formal methodology for dataset selection, akin to bibliographic research.

Purpose of the Study:

  • Introduce datagraphy, a structured approach for systematic dataset identification and evaluation.
  • Formalize dataset search as a research practice to enhance transparency, reproducibility, and collaboration.
  • Address challenges in dataset discovery and reuse within the big data ecosystem.

Main Methods:

  • Developed a nine-step framework to operationalize datagraphy.
  • Applied the framework through a datagraphic search focused on the exposome.
  • Analyzed challenges including metadata availability, repository heterogeneity, and dataset quality.

Main Results:

  • Datagraphy provides a systematic foundation for identifying and synthesizing reusable datasets.
  • The framework can enhance transparency, reproducibility, and efficiency at the researcher level.
  • Identified key challenges in metadata, repositories, accessibility, and quality impacting datagraphy.

Conclusions:

  • Datagraphy complements repository improvements by standardizing researcher-level practices.
  • Integrating datagraphy with FAIR principles and technological advancements can enable automated discovery and sustainable data reuse.
  • This structured methodology offers a scalable approach for FAIR-aligned, data-driven research across disciplines.