Satellite

Two decades of fumigation data from the Soybean Free Air Concentration Enrichment facility

  • Elise Kole Aspray
  • Timothy A. Mies
  • Elizabeth A. Ainsworth
Data Descriptor

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  • Genomics data for plant ecology, conservation and agriculture

    Scientific Data is open to submissions for this special collection: Genomics data for plant ecology, conservation and agriculture

    Open for submissions
  • Medical imaging data for digital diagnostics

    Scientific Data is open to submissions for this special collection: Medical imaging data for digital diagnostics

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  • The solution of the longstanding “protein folding problem” in 2021 showcased the transformative capabilities of AI in advancing the biomedical sciences. AI was characterized as successfully learning from protein structure data, which then spurred a more general call for AI-ready datasets to drive forward medical research. Here, we argue that it is the broad availability of knowledge, not just data, that is required to fuel further advances in AI in the scientific domain. This represents a quantum leap in a trend toward knowledge democratization that had already been developing in the biomedical sciences: knowledge is no longer primarily applied by specialists in a sub-field of biomedicine, but rather multidisciplinary teams, diverse biomedical research programs, and now machine learning. The development and application of explicit knowledge representations underpinning democratization is becoming a core scientific activity, and more investment in this activity is required if we are to achieve the promise of AI.

    • Christophe Dessimoz
    • Paul D. Thomas
    CommentOpen Access
  • As the number of cloud platforms supporting scientific research grows, there is an increasing need to support interoperability between two or more cloud platforms. A well accepted core concept is to make data in cloud platforms Findable, Accessible, Interoperable and Reusable (FAIR). We introduce a companion concept that applies to cloud-based computing environments that we call a Secure and Authorized FAIR Environment (SAFE). SAFE environments require data and platform governance structures and are designed to support the interoperability of sensitive or controlled access data, such as biomedical data. A SAFE environment is a cloud platform that has been approved through a defined data and platform governance process as authorized to hold data from another cloud platform and exposes appropriate APIs for the two platforms to interoperate.

    • Robert L. Grossman
    • Rebecca R. Boyles
    • Stan Ahalt
    CommentOpen Access
  • The ongoing debate on secondary use of health data for research has been renewed by the passage of comprehensive data privacy laws that shift control from institutions back to the individuals on whom the data was collected. Rights-based data privacy laws, while lauded by individuals, are viewed as problematic for the researcher due to the distributed nature of data control. Efforts such as the European Health Data Space initiative seek to build a new mechanism for secondary use that erodes individual control in favor of broader secondary use for beneficial health research. Health information sharing platforms do exist that embrace rights-based data privacy while simultaneously providing a rich research environment for secondary data use. The benefits of embracing rights-based data privacy to promote transparency of data use along with control of one’s participation builds the trust necessary for more inclusive/diverse/representative clinical research.

    • Scott D. Kahn
    • Sharon F. Terry
    CommentOpen Access
  • Data harmonization is an important method for combining or transforming data. To date however, articles about data harmonization are field-specific and highly technical, making it difficult for researchers to derive general principles for how to engage in and contextualize data harmonization efforts. This commentary provides a primer on the tradeoffs inherent in data harmonization for researchers who are considering undertaking such efforts or seek to evaluate the quality of existing ones. We derive this guidance from the extant literature and our own experience in harmonizing data for the emergent and important new field of COVID-19 public health and safety measures (PHSM).

    • Cindy Cheng
    • Luca Messerschmidt
    • Joan Barceló
    CommentOpen Access
  • Recent advances in computer-aided diagnosis, treatment response and prognosis in radiomics and deep learning challenge radiology with requirements for world-wide methodological standards for labeling, preprocessing and image acquisition protocols. The adoption of these standards in the clinical workflows is a necessary step towards generalization and interoperability of radiomics and artificial intelligence algorithms in medical imaging.

    • Miriam Cobo
    • Pablo Menéndez Fernández-Miranda
    • Lara Lloret Iglesias
    CommentOpen Access
  • Software and data citation are emerging best practices in scholarly communication. This article provides structured guidance to the academic publishing community on how to implement software and data citation in publishing workflows. These best practices support the verifiability and reproducibility of academic and scientific results, sharing and reuse of valuable data and software tools, and attribution to the creators of the software and data. While data citation is increasingly well-established, software citation is rapidly maturing. Software is now recognized as a key research result and resource, requiring the same level of transparency, accessibility, and disclosure as data. Software and data that support academic or scientific results should be preserved and shared in scientific repositories that support these digital object types for discovery, transparency, and use by other researchers. These goals can be supported by citing these products in the Reference Section of articles and effectively associating them to the software and data preserved in scientific repositories. Publishers need to markup these references in a specific way to enable downstream processes.

    • Shelley Stall
    • Geoffrey Bilder
    • Timothy Clark
    CommentOpen Access