Recognizing the value of software: a software citation guide

Transparency in research: An analysis of ChatGPT usage acknowledgment by authors across disciplines and geographies

This investigation systematically reviews the recognition of generative AI tools, particularly ChatGPT, in scholarly literature. Utilizing 1,226 publications from the Dimensions database, ranging from November 2022 to July 2023, the research scrutinizes temporal trends and distribution across disciplines and regions. U.S.-based authors lead in acknowledgments, with notable contributions from China and India. Predominantly, Biomedical and Clinical Sciences, as well as Information and Computing Sciences, are engaging with these AI tools. Publications like "The Lancet Digital Health" and platforms such as "bioRxiv" are recurrent venues for such acknowledgments, highlighting AI's growing impact on research dissemination. The analysis is confined to the Dimensions database, thus potentially overlooking other sources and grey literature. Additionally, the study abstains from examining the acknowledgments' quality or ethical considerations. Findings are beneficial for stakeholders, providing a basis for policy and scholarly discourse on ethical AI use in academia. This study represents the inaugural comprehensive empirical assessment of AI acknowledgment patterns in academic contexts, addressing a previously unexplored aspect of scholarly communication.

Publication Ethics in the Era of Artificial Intelligence

The application of new technologies, such as artificial intelligence (AI), to science affects the way and methodology in which research is conducted. While the responsible use of AI brings many innovations and benefits to science and humanity, its unethical use poses a serious threat to scientific integrity and literature. Even in the absence of malicious use, the Chatbot output itself, as a software application based on AI, carries the risk of containing biases, distortions, irrelevancies, misrepresentations and plagiarism. Therefore, the use of complex AI algorithms raises concerns about bias, transparency and accountability, requiring the development of new ethical rules to protect scientific integrity. Unfortunately, the development and writing of ethical codes cannot keep up with the pace of development and implementation of technology. The main purpose of this narrative review is to inform readers, authors, reviewers and editors about new approaches to publication ethics in the era of AI. It specifically focuses on tips on how to disclose the use of AI in your manuscript, how to avoid publishing entirely AI-generated text, and current standards for retraction.

Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles tailored for research software have been proposed by the FAIR for Research Software (FAIR4RS) Working Group. They provide a foundation for optimizing the reuse of research software. The FAIR4RS principles are, however, aspirational and do not provide practical instructions to the researchers. To fill this gap, we propose in this work the first actionable step-by-step guidelines for biomedical researchers to make their research software compliant with the FAIR4RS principles. We designate them as the FAIR Biomedical Research Software (FAIR-BioRS) guidelines. Our process for developing these guidelines, presented here, is based on an in-depth study of the FAIR4RS principles and a thorough review of current practices in the field. To support researchers, we have also developed a workflow that streamlines the process of implementing these guidelines. This workflow is incorporated in FAIRshare, a free and open-source software application aimed at simplifying the curation and sharing of FAIR biomedical data and software through user-friendly interfaces and automation. Details about this tool are also presented.

The role of metadata in reproducible computational research

Reproducible computational research (RCR) is the keystone of the scientific method for in silico analyses, packaging the transformation of raw data to published results. In addition to its role in research integrity, improving the reproducibility of scientific studies can accelerate evaluation and reuse. This potential and wide support for the FAIR principles have motivated interest in metadata standards supporting reproducibility. Metadata provide context and provenance to raw data and methods and are essential to both discovery and validation. Despite this shared connection with scientific data, few studies have explicitly described how metadata enable reproducible computational research. This review employs a functional content analysis to identify metadata standards that support reproducibility across an analytic stack consisting of input data, tools, notebooks, pipelines, and publications. Our review provides background context, explores gaps, and discovers component trends of embeddedness and methodology weight from which we derive recommendations for future work.