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Journal articles on the topic 'Scientific workflow and FAIR protocols'

Author: Grafiati

Published: 25 May 2024

Last updated: 31 July 2025

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1

Celebi, Remzi, Joao Rebelo Moreira, Ahmed A. Hassan, et al. "Towards FAIR protocols and workflows: the OpenPREDICT use case." PeerJ Computer Science 6 (September 21, 2020): e281. http://dx.doi.org/10.7717/peerj-cs.281.

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It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR prin

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2

Yuen, Denis, Louise Cabansay, Andrew Duncan, et al. "The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols." Nucleic Acids Research 49, W1 (2021): W624—W632. http://dx.doi.org/10.1093/nar/gkab346.

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Abstract Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a

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Soiland-Reyes, Stian, Peter Sefton, Leyla Jael Castro, et al. "Creating lightweight FAIR Digital Objects with RO-Crate." Research Ideas and Outcomes 8 (October 12, 2022): e93937. https://doi.org/10.3897/rio.8.e93937.

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RO-Crate (Soiland-Reyes et al. 2022) is a lightweight method to package research outputs along with their metadata, based on Linked Data principles (Bizer et al. 2009) and W3C standards. RO-Crate provides a flexible mechanism for researchers archiving and publishing rich data packages (or any other research outcome) by capturing their dependencies and context. However, additional measures should be taken to ensure that a crate is also following the FAIR principles (Wilkinson 2016), including consistent use of persistent identifiers, provenance, community standards, clear machine/human-readable

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Mozzherin, Dmitry, Deborah Paul, and Amanda Whitmire. "Can We Standardize Name Reconciliaton via OpenRefine?" Biodiversity Information Science and Standards 8 (August 19, 2024): e134910. https://doi.org/10.3897/biss.8.134910.

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Scientific names in biodiversity represent one of the oldest identifiers used in science. As a result, a common repetitive task is being able to reconcile a list of scientific names against curated data sources. Reconciliation allows one to determine if names in a list are spelled correctly, whether they are currently accepted, and their nomenclatural status. There are several online and local resources that provide reconciliation services. We share here the potential in interoperability across reconciliation tools.Global Names Verifier (GNverifier), Catalogue of Life, Global Biodiversity Info

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Rios, Nelson, Sharif Islam, James Macklin, and Andrew Bentley. "Technical Considerations for a Transactional Model to Realize the Digital Extended Specimen." Biodiversity Information Science and Standards 5 (September 3, 2021): e73812. https://doi.org/10.3897/biss.5.73812.

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Technological innovations over the past two decades have given rise to the online availability of more than 150 million specimen and species-lot records from biological collections around the world through large-scale biodiversity data-aggregator networks. In the present landscape of biodiversity informatics, collections data are captured and managed locally in a wide variety of databases and collection management systems and then shared online as point-in-time Darwin Core archive snapshots. Data providers may publish periodic revisions to these data files, which are retrieved, processed and r

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Penev, Lyubomir, Dimitrios Koureas, Quentin Groom, et al. "The Biodiversity Knowledge Hub (BKH): a crosspoint and knowledge broker for FAIR and linked biodiversity data." Biodiversity Information Science and Standards 7 (August 24, 2023): e111482. https://doi.org/10.3897/biss.7.111482.

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The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated biodiversity knowledge graph and an emerging new community of users. The BKH is aimed at biodiversity researchers in the widest sense, research infra

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Dillen, Mathias, Pieter Huybrechts, Quentin Groom, and Lynn Delgat. "Calculating the Digitization Level of Specimens with the Minimum Information about a Digital Specimen (MIDS) Standard." Biodiversity Information Science and Standards 6 (August 1, 2022): e90879. https://doi.org/10.3897/biss.6.90879.

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Natural history specimens constitute physical evidence for past observations of nature. They hold further value as the backbone of taxonomy and as historical samples that can be subjected to further analysis. Yet, as physical objects scattered across collections around the world, their scientific use cases are limited by an overall lack of FAIRness, i.e. not easily Findable, Accessible, Interoperable or Reusable. Digitization of these specimens through imaging and categorical metadata capture can improve this FAIRness and has been done to some extent for decades already, but only recently have

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8

Peterseil, Johannes, Alexandre Belleflamme, Alessandro Oggioni, et al. "Advancing Scientific Research through Well-Defined and Standardized Data Products in eLTER." ARPHA Conference Abstracts 8 (May 28, 2025): e151888. https://doi.org/10.3897/aca.8.e151888.

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The scientific community increasingly relies on high-quality data products to drive research, enable cross-disciplinary studies and inform decision-making. The eLTER RI, as a European scale research infrastructure, aims to monitor the key characteristics of ecosystems and biodiversity and their response to global change and provide data streams as one of its services. In this context, the Whole System Approach (WAILS) and the derived eLTER Standard Observations (SOs) provide the scientific framework and protocols not only for data collection but also for integrating legacy data from long-term

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Zulfiqar, Mahnoor, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck, Kristian Peters, and Luiz Gadelha. "Implementation of FAIR Practices in Computational Metabolomics Workflows—A Case Study." Metabolites 14, no. 2 (2024): 118. http://dx.doi.org/10.3390/metabo14020118.

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Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on Workfl

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Hemani, Yousuf, Kilian Koch, Oscar Mendo-Diaz, Anusch Bachhofner, Simone Baffelli, and Davide Bleiner. "The openBIS Digital Platform for Instrumentation and Data Workflow in the Analytical Laboratory." CHIMIA 79, no. 1-2 (2025): 36–45. https://doi.org/10.2533/chimia.2025.36.

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The management of scientific data plays a key role in all research areas and has increased in importance. Providing researchers with customizable data management tools is crucial for effectively managing data according to the FAIR principles. These principles have been defined by Wilkinson et al. in 2016, which describe how scientific data should be managed.[1] To support the specific needs of researchers at Empa, openBIS[2] was chosen as a FAIR compliant data management platform. OpenBIS is an Electronic Laboratory Notebook (ELN) and Laboratory Information Management System (LIMS) developed a

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Sinaci, A. Anil, Francisco J. Núñez-Benjumea, Mert Gencturk, et al. "From Raw Data to FAIR Data: The FAIRification Workflow for Health Research." Methods of Information in Medicine 59, S 01 (2020): e21-e32. http://dx.doi.org/10.1055/s-0040-1713684.

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Abstract Background FAIR (findability, accessibility, interoperability, and reusability) guiding principles seek the reuse of data and other digital research input, output, and objects (algorithms, tools, and workflows that led to that data) making them findable, accessible, interoperable, and reusable. GO FAIR - a bottom-up, stakeholder driven and self-governed initiative - defined a seven-step FAIRification process focusing on data, but also indicating the required work for metadata. This FAIRification process aims at addressing the translation of raw datasets into FAIR datasets in a general

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Nayyar, Anand, Rudra Rameshwar, and Piyush Kanti Dutta. "Special Issue on Recent Trends and Future of Fog and Edge Computing, Services and Enabling Technologies." Scalable Computing: Practice and Experience 20, no. 2 (2019): iii—vi. http://dx.doi.org/10.12694/scpe.v20i2.1558.

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Recent Trends and Future of Fog and Edge Computing, Services, and Enabling Technologies Cloud computing has been established as the most popular as well as suitable computing infrastructure providing on-demand, scalable and pay-as-you-go computing resources and services for the state-of-the-art ICT applications which generate a massive amount of data. Though Cloud is certainly the most fitting solution for most of the applications with respect to processing capability and storage, it may not be so for the real-time applications. The main problem with Cloud is the latency as the Cloud dat

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13

de Visser, Casper, Lennart F. Johansson, Purva Kulkarni, et al. "Ten quick tips for building FAIR workflows." PLOS Computational Biology 19, no. 9 (2023): e1011369. http://dx.doi.org/10.1371/journal.pcbi.1011369.

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Research data is accumulating rapidly and with it the challenge of fully reproducible science. As a consequence, implementation of high-quality management of scientific data has become a global priority. The FAIR (Findable, Accesible, Interoperable and Reusable) principles provide practical guidelines for maximizing the value of research data; however, processing data using workflows—systematic executions of a series of computational tools—is equally important for good data management. The FAIR principles have recently been adapted to Research Software (FAIR4RS Principles) to promote the repro

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Albtoush, Alaa, Farizah Yunus, Khaled Almi’ani, and Noor Maizura Mohamad Noor. "Structure-Aware Scheduling Methods for Scientific Workflows in Cloud." Applied Sciences 13, no. 3 (2023): 1980. http://dx.doi.org/10.3390/app13031980.

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Scientific workflows consist of numerous tasks subject to constraints on data dependency. Effective workflow scheduling is perpetually necessary to efficiently utilize the provided resources to minimize workflow execution cost and time (makespan). Accordingly, cloud computing has emerged as a promising platform for scheduling scientific workflows. In this paper, level- and hierarchy-based scheduling approaches were proposed to address the problem of scheduling scientific workflow in the cloud. In the level-based approach, tasks are partitioned into a set of isolated groups in which available v

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Mahmoudi, Morteza, Saya Ameli, and Sherry Moss. "The urgent need for modification of scientific ranking indexes to facilitate scientific progress and diminish academic bullying." BioImpacts 10, no. 1 (2019): 5–7. http://dx.doi.org/10.15171/bi.2019.30.

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Academic bullying occurs when senior scientists direct abusive behavior such as verbal insults, public shaming, isolation, and threatening toward vulnerable junior colleagues such as postdocs, graduate students and lab members. We believe that one root cause of bullying behavior is the pressure felt by scientists to compete for rankings designed to measure their scientific worth. These ratings, such as the h-index, have several unintended consequences, one of which we believe is academic bullying. Under pressure to achieve higher and higher rankings, in exchange for positive evaluations, grant

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Ammar, Ammar, Serena Bonaretti, Laurent Winckers, et al. "A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences." Nanomaterials 10, no. 10 (2020): 2068. http://dx.doi.org/10.3390/nano10102068.

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Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the lif

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Ayoubi, Doaa. "Investigational drugs services pharmacists education and workflow structure." JCO Global Oncology 9, Supplement_1 (2023): 169. http://dx.doi.org/10.1200/go.2023.9.supplement_1.169.

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169 Background: Per NIH U.S. National Library of Medicine, 428,103 research studies are registered globally as of September 19th, 2022. Each institution must assess its institutional readiness as the complexity and volume of clinical trial increases. Institutional readiness helps assess the capacity of an institution to adopt new technologies and policies to accept, activate, and adjust research despite the complexity of the clinical trial. Clinical research pharmacists help improve the safety and quality of the research by reviewing the scientific literature and medication-related information

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18

Velterop, Jan, and Erik Schultes. "An Academic Publishers’ GO FAIR Implementation Network (APIN)." Information Services & Use 40, no. 4 (2021): 333–41. http://dx.doi.org/10.3233/isu-200102.

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Presented here is a proposal for the academic publishing industry to get actively involved in the formulation of protocols and standards that make published scientific research material machine-readable in order to facilitate data to be findable, accessible, interoperable, and re-usable (FAIR). Given the importance of traditional journal publications in scholarly communication worldwide, active involvement of academic publishers in advancing the more routine creation and reuse of FAIR data is highly desired.

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Siew, C. B., and A. Abdul Rahman. "3D STREAMING PROTOCOLS FOR SPATIAL DATA INFRASTRUCTURE: A BRIEF REVIEW." ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences XLII-4/W1 (September 29, 2016): 23–24. http://dx.doi.org/10.5194/isprs-archives-xlii-4-w1-23-2016.

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Web services utilizations in Spatial Data Infrastructure (SDI) have been well established and standardized by Open Geospatial 3D graphics rendering has been a topic of interest among scientific domain from both computer science and geospatial science. Different methods were proposed and discussed in these researches for different domains and applications. Each method provides advantages and trade-offs. Some methods proposed image based rendering for 3D graphics and ultimately. This paper attempts to discuss several techniques from past researches and attempts to propose another method inspired

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Alvarez-Romero, Celia, Alicia Martínez-García, A. Anil Sinaci, et al. "FAIR4Health: Findable, Accessible, Interoperable and Reusable data to foster Health Research." Open Research Europe 2 (May 31, 2022): 34. http://dx.doi.org/10.12688/openreseurope.14349.2.

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Due to the nature of health data, its sharing and reuse for research are limited by ethical, legal and technical barriers. The FAIR4Health project facilitated and promoted the application of FAIR principles in health research data, derived from the publicly funded health research initiatives to make them Findable, Accessible, Interoperable, and Reusable (FAIR). To confirm the feasibility of the FAIR4Health solution, we performed two pathfinder case studies to carry out federated machine learning algorithms on FAIRified datasets from five health research organizations. The case studies demonstr

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Alvarez-Romero, Celia, Alicia Martínez-García, A. Anil Sinaci, et al. "FAIR4Health: Findable, Accessible, Interoperable and Reusable data to foster Health Research." Open Research Europe 2 (March 9, 2022): 34. http://dx.doi.org/10.12688/openreseurope.14349.1.

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Due to the nature of health data, its sharing and reuse for research are limited by ethical, legal and technical barriers. The FAIR4Health project facilitated and promoted the application of FAIR principles in health research data, derived from the publicly funded health research initiatives to make them Findable, Accessible, Interoperable, and Reusable (FAIR). To confirm the feasibility of the FAIR4Health solution, we performed two pathfinder case studies to carry out federated machine learning algorithms on FAIRified datasets from five health research organizations. The case studies demonstr

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Livermore, Laurence, Paul Brack, Ben Scott, Stian Soiland-Reyes, and Oliver Woolland. "The Specimen Data Refinery: Using a scientific workflow approach for information extraction." Biodiversity Information Science and Standards 6 (August 23, 2022): e93500. https://doi.org/10.3897/biss.6.93500.

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Over the past three years, we have been developing the Specimen Data Refinery (SDR) to automate the extraction of data from specimen images as part of the SYNTHESYS project (Walton et al. 2020). The SDR provides an easy to deploy, open source, web-based interface to multiple workflows that enable a user to create new or enhance existing natural history specimen records. The SDR uses the Galaxy workflow platform as the basis for managing data analysis, and where possible, using existing Galaxy community tools and approaches (Jalili et al. 2020, Hardisty et al. 2022). We have developed a library

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Costa, Kleber Ferreira, Maria Cristina Elyote M. Santos, Michela Caroline Macedo, and Paulo César Marques de Andrade Santos. "Between Methodological Agility and Participant Protection: Opinion Research and Scientific Ethics in Light of FAIR Principles and Brazilian Legal Frameworks." Revista de Gestão Social e Ambiental 19, no. 4 (2025): e011794. https://doi.org/10.24857/rgsa.v19n4-051.

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Objective: This study analyzes the relationship between public opinion research and scientific ethics, focusing on the role of Research Ethics Committees (RECs), seeking to examine how ethical protocols, regulated by the Resolutions of the National Health Council (466/2012; 510/2016) and Law 14.874/2024, ensure participant protection and methodological quality. Theoretical Framework: Contemporary scientific research requires the integration of ethical and methodological principles, especially in research involving human subjects. FAIR (Findable, Accessible, Interoperable, Reusable) data manage

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Griswold, Michael, James Henegan, Chad Blackshear, et al. "FAIR SHARING OF THE BLSA DATA ECOSYSTEM." Innovation in Aging 6, Supplement_1 (2022): 311. http://dx.doi.org/10.1093/geroni/igac059.1231.

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Abstract The BLSA is an invaluable resource for the study of human aging with uniquely rich measures taken longitudinally on a continuous replenishment cohort since 1958. Tremendous interest has been expressed by the United States and international research communities in expanded access to and use of BLSA data to address emerging scientific questions. Here, we will describe recent study leadership initiatives into: (1) making the BLSA data more FAIR (Findable, Accessible, Interoperable, and Reusable), (2) growing a BLSA data ecosystem that enables scalable sharing, and (3) leveraging and deve

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GUIDOTI, MARCUS, FELIPE LORENZ SIMÕES, TATIANA PETERSEN RUSCHEL, VALDENAR DA ROSA GONÇALVES, CAROLINA SOKOLOWICZ, and DONAT AGOSTI. "Using taxonomic treatments to assess an author’s career: the impactful Jocélia Grazia." Zootaxa 4958, no. 1 (2021): 12–33. http://dx.doi.org/10.11646/zootaxa.4958.1.4.

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Here we present a descriptive analysis of the bibliographic production of the world-renowned heteropterist Dr. Jocélia Grazia and comments on her taxonomic reach based on extracted taxonomic treatments. We analyzed a total of 219 published documents, including scientific papers, scientific notes, and book chapters. Additionally, we applied the Plazi workflow to extract taxonomic treatments, images, tables, treatment citations and materials citations, and references from 75 different documents in accordance with the FAIR (Findability, Accessibility, Interoperability, and Reuse) principles and m

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Niehues, Anna, Visser Casper de, Fiona Hagenbeek, et al. "A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object." Research Ideas and Outcomes 8 (August 25, 2022): e94042. https://doi.org/10.3897/rio.8.e94042.

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In current biomedical and complex trait research, increasing numbers of large molecular profiling (omics) data sets are being generated. At the same time, many studies fail to be reproduced (Baker 2016, Kim 2018). In order to improve study reproducibility and data reuse, including integration of data sets of different types and origins, it is imperative to work with omics data that is findable, accessible, interoperable, and reusable (FAIR, Wilkinson 2016) at the source. The data analysis, integration and stewardship pillar of the Netherlands X-omics Initiative aims to facilitate multi-omics r

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Kochev, Nikolay, Nina Jeliazkova, Vesselina Paskaleva, et al. "Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database." Nanomaterials 10, no. 10 (2020): 1908. http://dx.doi.org/10.3390/nano10101908.

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The field of nanoinformatics is rapidly developing and provides data driven solutions in the area of nanomaterials (NM) safety. Safe by Design approaches are encouraged and promoted through regulatory initiatives and multiple scientific projects. Experimental data is at the core of nanoinformatics processing workflows for risk assessment. The nanosafety data is predominantly recorded in Excel spreadsheet files. Although the spreadsheets are quite convenient for the experimentalists, they also pose great challenges for the consequent processing into databases due to variability of the templates

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Kochev, Nikolay, Nina Jeliazkova, Vesselina Paskaleva, et al. "Your Spreadsheets Can Be FAIR: A Tool and FAIRification Workflow for the eNanoMapper Database." MDPI Nanomaterials 10, no. 10 (2020): 1908. https://doi.org/10.3390/nano10101908.

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The field of nanoinformatics is rapidly developing and provides data driven solutions in the area of nanomaterials (NM) safety. Safe by Design approaches are encouraged and promoted through regulatory initiatives and multiple scientific projects. Experimental data is at the core of nanoinformatics processing workflows for risk assessment. The nanosafety data is predominantly recorded in Excel spreadsheet files. Although the spreadsheets are quite convenient for the experimentalists, they also pose great challenges for the consequent processing into databases due to variability of the templates

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Hernandez, Mikel, Gorka Epelde, Andoni Beristain, et al. "Incorporation of Synthetic Data Generation Techniques within a Controlled Data Processing Workflow in the Health and Wellbeing Domain." Electronics 11, no. 5 (2022): 812. http://dx.doi.org/10.3390/electronics11050812.

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To date, the use of synthetic data generation techniques in the health and wellbeing domain has been mainly limited to research activities. Although several open source and commercial packages have been released, they have been oriented to generating synthetic data as a standalone data preparation process and not integrated into a broader analysis or experiment testing workflow. In this context, the VITALISE project is working to harmonize Living Lab research and data capture protocols and to provide controlled processing access to captured data to industrial and scientific communities. In thi

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Soundarajan, Sanjay, Sachira Kuruppu, Ashutosh Singh, Jongchan Kim, and Monalisa Achalla. "SPARClink: an interactive tool to visualize the impact of the SPARC program." F1000Research 11 (January 31, 2022): 124. http://dx.doi.org/10.12688/f1000research.75071.1.

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The National Institutes of Health (NIH) Stimulating Peripheral Activity to Relieve Conditions (SPARC) program seeks to accelerate the development of therapeutic devices that modulate electrical activity in nerves to improve organ function. SPARC-funded researchers are generating rich datasets from neuromodulation research that are curated and shared according to FAIR (Findable, Accessible, Interoperable, and Reusable) guidelines and are accessible to the public on the SPARC data portal. Keeping track of the utilization of these datasets within the larger research community is a feature that wi

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Wong, Ambrose H., Jessica M. Ray, Marc A. Auerbach, et al. "Study protocol for the ACT response pilot intervention: development, implementation and evaluation of a systems-based Agitation Code Team (ACT) in the emergency department." BMJ Open 10, no. 6 (2020): e036982. http://dx.doi.org/10.1136/bmjopen-2020-036982.

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IntroductionEmergency department (ED) visits for behavioural conditions are rising, with 1.7 million associated episodes of patient agitation occurring annually in acute care settings. When de-escalation techniques fail during agitation management, patients are subject to use of physical restraints and sedatives, which are associated with up to 37% risk of hypotension, apnoea and physical injuries. At the same time, ED staff report workplace violence due to physical assaults during agitation events. We recently developed a theoretical framework to characterise ED agitation, which identified te

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Pouchard, Line, Tanzima Islam, and Bogdan Nicolae. "Challenges for Implementing FAIR Digital Objects with High Performance Workflows." Research Ideas and Outcomes 8 (October 12, 2022): e94835. https://doi.org/10.3897/rio.8.e94835.

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New types of workflows are being used in science that couple traditional distributed and high-performance computing (HPC) with data-intensive approaches, and orchestrate ensembles of numerical simulations and artificial intelligence (AI) models. Such workflows may use AI models to supplement computation where numerical simulations may be too computationally expensive, to automate trivial yet time consuming operations, to perform preliminary selections among intractable numbers of combinations in domains as diverse as protein binding, fine-grid climate simulations, and drug discovery. They offe

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De, Geest Paul, Frederik Coppens, Stian Soiland-Reyes, Ignacio Eguinoa, and Simone Leo. "Enhancing RDM in Galaxy by integrating RO-Crate." Research Ideas and Outcomes 8 (October 12, 2022): e95164. https://doi.org/10.3897/rio.8.e95164.

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We introduce how the Galaxy research environment (Jalili et al. 2020) integrates with RO-Crate as an implementation of Findable Accessible Interoperable Reproducible Digital Objects (FAIR Digital Objects / FDO) (Wilkinson et al. 2016, Schultes and Wittenburg 2018) and how using RO-Crate as an exchange mechanism of workflows and their execution history helps integrate Galaxy with the wider ecosystem of ELIXIR (Harrow et al. 2021) and the European Open Science Cloud (EOSC-Life) to enable FAIR and reproducible data analysis.RO-Crate (Soiland-Reyes et al. 2022) is a generic packaging format contai

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Thompson, Karen, and Joanne Birch. "Mapping the Digitisation Workflow in a University Herbarium." Research Ideas and Outcomes 9 (August 18, 2023): e106883. https://doi.org/10.3897/rio.9.e106883.

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Specimens or objects in natural history collections hold substantial research and cultural value that is enhanced where these items are made digitally available. Benefits of digitisation include increasing open access to collection-based biodiversity data, increasing productivity of scientific research, enabling novel research applications of digitally accessible data, reducing preservation requirements through reduced object handling, and expanding potential for "remote curation" in collections. However, the time available for object and data digitisation is limited for most collections. Well

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Mascarenhas, Miguel, Miguel Martins, Tiago Ribeiro, et al. "Software as a Medical Device (SaMD) in Digestive Healthcare: Regulatory Challenges and Ethical Implications." Diagnostics 14, no. 18 (2024): 2100. http://dx.doi.org/10.3390/diagnostics14182100.

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The growing integration of software in healthcare, particularly the rise of standalone software as a medical device (SaMD), is transforming digestive medicine, a field heavily reliant on medical imaging for both diagnosis and therapeutic interventions. This narrative review aims to explore the impact of SaMD on digestive healthcare, focusing on the evolution of these tools and their regulatory and ethical challenges. Our analysis highlights the exponential growth of SaMD in digestive healthcare, driven by the need for precise diagnostic tools and personalized treatment strategies. This rapid a

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Giora, Julia, Donat Agosti, Tatiana Ruschel, and Jonas Castro. "Engaging the Scientific Community, Authors and Publishers in FAIR Taxonomic Data Liberation: An overview of training resources at Plazi." Biodiversity Information Science and Standards 7 (August 9, 2023): e110695. https://doi.org/10.3897/biss.7.110695.

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Since 2008, the not-for-profit organization Plazi*1, based in Switzerland, has been supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To achieve this goal, Plazi makes use of in-house software tools for data mining and extraction from taxonomic publications, along with other partner institutions' tools and platforms, to liberate data on animals, plants, fungi, and more. In its mission to make taxonomic data FAIRly (Findable, Accessible, Interoperable and Reusable*2) available to the community, Plazi has developed sets of training materia

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Furxhi, Irini, Antti Joonas Koivisto, Finbarr Murphy, Sara Trabucco, Benedetta Del Secco, and Athanasios Arvanitis. "Data Shepherding in Nanotechnology. The Exposure Field Campaign Template." Nanomaterials 11, no. 7 (2021): 1818. http://dx.doi.org/10.3390/nano11071818.

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In this paper, we demonstrate the realization process of a pragmatic approach on developing a template for capturing field monitoring data in nanomanufacturing processes. The template serves the fundamental principles which make data scientifically Findable, Accessible, Interoperable and Reusable (FAIR principles), as well as encouraging individuals to reuse it. In our case, the data shepherds’ (the guider of data) template creation workflow consists of the following steps: (1) Identify relevant stakeholders, (2) Distribute questionnaires to capture a general description of the data to be gene

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Giglia, Elena. "Open? The only way forward for science." Journal of Open Access to Law 11, no. 1 (2023): 12. https://doi.org/10.63567/j3ns0922.

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This paper aims to set out the reasons underlying the need to foster as much as possible the sharing and re-use of research data as well as their FAIRness, taking into account the various interests at stake. COVID-19 showed that sharing is the only way to go and that to advance science we need data – and every bit of the research process -, not only the final synthesis of the research itself, i.e., the article on a scientific journal. Scientific journals are still at the core of research evaluation, which is being reformed to include any research output and to reward collaboration. To be openl

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Gomez-Diaz, Teresa, and Tomas Recio. "Research Software vs. Research Data II: Protocols for Research Data dissemination and evaluation in the Open Science context." F1000Research 11 (October 7, 2022): 117. http://dx.doi.org/10.12688/f1000research.78459.2.

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Background: Open Science seeks to render research outputs visible, accessible and reusable. In this context, Research Data and Research Software sharing and dissemination issues provide real challenges to the scientific community, as consequence of recent progress in political, legal and funding requirements. Methods: We take advantage from the approach we have developed in a precedent publication, in which we have highlighted the similarities between the Research Data and Research Software definitions. Results: The similarities between Research Data and Research Software definitions can be ex

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Gomez-Diaz, Teresa, and Tomas Recio. "Research Software vs. Research Data II: Protocols for Research Data dissemination and evaluation in the Open Science context." F1000Research 11 (January 28, 2022): 117. http://dx.doi.org/10.12688/f1000research.78459.1.

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Background: Open Science seeks to render research outputs visible, accessible and reusable. In this context, Research Data and Research Software sharing and dissemination issues provide real challenges to the scientific community, as consequence of recent progress in political, legal and funding requirements. Methods: We take advantage from the approach we have developed in a precedent publication, in which we have highlighted the similarities between the Research Data and Research Software definitions. Results: The similarities between Research Data and Research Software definitions can be ex

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Martinou, Eirini, and Angeliki Angelidi. "The role of open research in improving the standards of evidence synthesis: current challenges and potential solutions in systematic reviews." F1000Research 11 (December 5, 2022): 1435. http://dx.doi.org/10.12688/f1000research.127179.1.

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Systematic reviews (SRs) and meta-analyses (MAs) are the cornerstone of evidence-based medicine and are placed at the top of the level-of-evidence pyramid. To date, there are several methodological resources available from international organizations such as the Cochrane Collaboration that aim to aid researchers in conducting high-quality secondary research and promoting reproducibility, transparency and scientific rigour. Nevertheless, researchers still face challenges in most stages of evidence synthesis. Open research and the FAIR (findability, accessibility, interoperability, and reusabili

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Fouilloux, Anne, Federica Foglini, and Elisa Trasatti. "FAIR Research Objects for realizing Open Science with RELIANCE EOSC project." Research Ideas and Outcomes 8 (August 25, 2022): e93940. https://doi.org/10.3897/rio.8.e93940.

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The H2020 <u>Reliance</u> project delivers a suite of innovative and interconnected services that extend European Open Science Cloud (EOSC)'s capabilities to support the management of the research lifecycle within Earth Science Communities and Copernicus Users. The project has delivered 3 complementary technologies: Research Objects (ROs), Data Cubes and AI-based Text Mining.<u>RoHub</u> is a Research Object management platform that implements these 3 technologies and enables researchers to collaboratively manage, share and preserve their research work.RoHub implements the full RO model and pa

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Tmušić, Goran, Salvatore Manfreda, Helge Aasen, et al. "Current Practices in UAS-based Environmental Monitoring." Remote Sensing 12, no. 6 (2020): 1001. http://dx.doi.org/10.3390/rs12061001.

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With the increasing role that unmanned aerial systems (UAS) are playing in data collection for environmental studies, two key challenges relate to harmonizing and providing standardized guidance for data collection, and also establishing protocols that are applicable across a broad range of environments and conditions. In this context, a network of scientists are cooperating within the framework of the Harmonious Project to develop and promote harmonized mapping strategies and disseminate operational guidance to ensure best practice for data collection and interpretation. The culmination of th

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Friedrichs, Virginia, Darwin Reicks, Jeffrey J. Zimmerman, et al. "Establishment of a Suitable Diagnostic Workflow to Ensure Sensitive Detection of African Swine Fever Virus Genome in Porcine Semen." Pathogens 13, no. 7 (2024): 537. http://dx.doi.org/10.3390/pathogens13070537.

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The rapid spread of African swine fever virus (ASFV), causing severe and often lethal disease in domestic pigs and Eurasian wild boar, continues to be a threat to pig populations and dependent industries. Despite scientific achievements that have deepened our understanding of ASFV pathogenesis, alternative transmission routes for ASFV remain to be elucidated. We previously demonstrated the efficient transmission of ASFV from infected boars to naïve recipient gilts via artificial insemination, thereby highlighting the importance of surveillance of boar semen prior to its shipment. Since the acc

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Svaluto-Ferro, Enea, Benjamin Kunz, Nukorn Plainpan, Graham Kimbell, Corsin Battaglia, and David Reber. "Towards an Autonomous Robotic Battery Materials Research Platform Powered by Automated Workflow and Ontologized FAIR Data Management." ECS Meeting Abstracts MA2025-01, no. 1 (2025): 96. https://doi.org/10.1149/ma2025-01196mtgabs.

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Today, only short individual segments of the experimental battery research & innovation cycle are automated, often requiring man-power-intensive intermediate process steps to complete the cycle. In addition, the outcome of lab-level battery research is often dependent on the researcher's skill level compromising reproducibility. Extending lab automation by combining multiple segments into automated application-relevant closed-loop sequences enables rapid testing of scientific hypotheses and validation of physical models. Besides reducing human error and improving reproducibility, this appr

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Butcher, David S., Christian J. Brigham, James Berhalter, et al. "Cybersecurity in a Large-Scale Research Facility—One Institution’s Approach." Journal of Cybersecurity and Privacy 3, no. 2 (2023): 191–208. http://dx.doi.org/10.3390/jcp3020011.

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A cybersecurity approach for a large-scale user facility is presented—utilizing the National High Magnetic Field Laboratory (NHMFL) at Florida State University (FSU) as an example. The NHMFL provides access to the highest magnetic fields for scientific research teams from a range of disciplines. The unique challenges of cybersecurity at a widely accessible user facility are showcased, and relevant cybersecurity frameworks for the complex needs of a user facility with industrial-style equipment and hazards are discussed, along with the approach for risk identification and management, which dete

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Akgül, Seçkin, Carolin Offenhäuser, Anja Kordowski, and Bryan W. Day. "Engineering Novel Lentiviral Vectors for Labelling Tumour Cells and Oncogenic Proteins." Bioengineering 9, no. 3 (2022): 91. http://dx.doi.org/10.3390/bioengineering9030091.

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Lentiviral vectors are unique and highly efficient genetic tools to incorporate genetic materials into the genome of a variety of cells whilst conserving biosafety. Their rapid acceptance made it necessary to improve existing protocols, including molecular engineering and cloning, production of purified lentiviral particles, and efficient infection of target cells. In addition to traditional protocols, which can be time-consuming, several biotechnology companies are providing scientists with commercially available lentiviral constructs and particles. However, these constructs are limited by th

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Zhang, Tianyi. "Protection of athletes’ rights and interests: Application of biomechanics in sports law and legal issues." Molecular & Cellular Biomechanics 22, no. 4 (2025): 1698. https://doi.org/10.62617/mcb1698.

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With the continuous refinement of sports law, the scientific safeguarding of athletes’ rights to fair competition and their physical and mental well-being has emerged as a critical issue. This study introduces an innovative approach that integrates biomechanical technologies with a multidimensional cloud model algorithm, applied within the realm of sports law. Its primary objective is to optimize refereeing decisions and prevent sports injuries through objective data analysis. The research employs track and field events as its experimental setting, where athlete data—including joint angular di

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Penev, Lyubomir, Tobias Kuhn, Wouter Addink, et al. "Nanopublications: Universal, Anti-Silo and FAIR Method for Publishing, Annotating and Sharing of Open Linked Data for Biodiversity." Biodiversity Information Science and Standards 8 (December 5, 2024): e143567. https://doi.org/10.3897/biss.8.143567.

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Nanopublications are the smallest units of published information that comply with all known requirements for Findable, Accessible, Interoperable, and Reusable (FAIR) Linked Open Data and are both human-readable and machine-actionable (Mons and Velterop 2009). Nanopublications can be used as a machine-readable complement to traditional research articles, allowing data to be attributed and cited, but also to be published as standalone scientific assertions bearing provenance on the authorship and publication date (Kuhn et al. 2021). During the Biodiversity Community Integrated Knowledge Library

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Soiland-Reyes, Stian, Peter Sefton, Leyla Jael Castro, et al. "Creating lightweight FAIR Digital Objects with RO-Crate." Research Ideas and Outcomes 8 (October 12, 2022). http://dx.doi.org/10.3897/rio.8.e93937.

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RO-Crate (Soiland-Reyes et al. 2022) is a lightweight method to package research outputs along with their metadata, based on Linked Data principles (Bizer et al. 2009) and W3C standards. RO-Crate provides a flexible mechanism for researchers archiving and publishing rich data packages (or any other research outcome) by capturing their dependencies and context. However, additional measures should be taken to ensure that a crate is also following the FAIR principles (Wilkinson 2016), including consistent use of persistent identifiers, provenance, community standards, clear machine/human-readable

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