PLANTdataHUB: a collaborative platform for continuous FAIR data sharing in plant research.

In modern reproducible, hypothesis-driven plant research, scientists are increasingly relying on research data management (RDM) services and infrastructures to streamline the processes of collecting, processing, sharing, and archiving research data. FAIR (i.e., findable, accessible, interoperable, and reusable) research data play a pivotal role in enabling the integration of interdisciplinary knowledge and facilitating the comparison and synthesis of a wide range of analytical findings. The PLANTdataHUB offers a solution that realizes RDM of scientific (meta)data as evolving collections of files in a directory - yielding FAIR digital objects called ARCs - with tools that enable scientists to plan, communicate, collaborate, publish, and reuse data on the same platform while gaining continuous quality control insights. The centralized platform is scalable from personal use to global communities and provides advanced federation capabilities for institutions that prefer to host their own satellite instances. This approach borrows many concepts from software development and adapts them to fit the challenges of the field of modern plant science undergoing digital transformation. The PLANTdataHUB supports researchers in each stage of a scientific project with adaptable continuous quality control insights, from the early planning phase to data publication. The central live instance of PLANTdataHUB is accessible at (https://git.nfdi4plants.org), and it will continue to evolve as a community-driven and dynamic resource that serves the needs of contemporary plant science.

A practical guide to bioimaging research data management in core facilities.

Bioimage data are generated in diverse research fields throughout the life and biomedical sciences. Its potential for advancing scientific progress via modern, data-driven discovery approaches reaches beyond disciplinary borders. To fully exploit this potential, it is necessary to make bioimaging data, in general, multidimensional microscopy images and image series, FAIR, that is, findable, accessible, interoperable and reusable. These FAIR principles for research data management are now widely accepted in the scientific community and have been adopted by funding agencies, policymakers and publishers. To remain competitive and at the forefront of research, implementing the FAIR principles into daily routines is an essential but challenging task for researchers and research infrastructures. Imaging core facilities, well-established providers of access to imaging equipment and expertise, are in an excellent position to lead this transformation in bioimaging research data management. They are positioned at the intersection of research groups, IT infrastructure providers, the institution´s administration, and microscope vendors. In the frame of German BioImaging - Society for Microscopy and Image Analysis (GerBI-GMB), cross-institutional working groups and third-party funded projects were initiated in recent years to advance the bioimaging community's capability and capacity for FAIR bioimage data management. Here, we provide an imaging-core-facility-centric perspective outlining the experience and current strategies in Germany to facilitate the practical adoption of the FAIR principles closely aligned with the international bioimaging community. We highlight which tools and services are ready to be implemented and what the future directions for FAIR bioimage data have to offer.

Setting up an institutional OMERO environment for bioimage data: Perspectives from both facility staff and users.

Modern bioimaging core facilities at research institutions are essential for managing and maintaining high-end instruments, providing training and support for researchers in experimental design, image acquisition and data analysis. An important task for these facilities is the professional management of complex multidimensional bioimaging data, which are often produced in large quantity and very different file formats. This article details the process that led to successfully implementing the OME Remote Objects system (OMERO) for bioimage-specific research data management (RDM) at the Core Facility Cellular Imaging (CFCI) at the Technische Universität Dresden (TU Dresden). Ensuring compliance with the FAIR (findable, accessible, interoperable, reusable) principles, we outline here the challenges that we faced in adapting data handling and storage to a new RDM system. These challenges included the introduction of a standardised group-specific naming convention, metadata curation with tagging and Key-Value pairs, and integration of existing image processing workflows. By sharing our experiences, this article aims to provide insights and recommendations for both individual researchers and educational institutions intending to implement OMERO as a management system for bioimaging data. We showcase how tailored decisions and structured approaches lead to successful outcomes in RDM practices.

Data Policy Finder: an easily integratable tool connecting data librarians with researchers to navigate publication requirements.

The Data Policy Finder is a searchable database containing librarian-curated information, links, direct quotes from relevant policy sections, and notes to help the researcher search, verify, and plan for their publication data requirements. The Memorial Sloan Kettering Cancer Center Library launched this new resource to help researchers navigate the ever-growing, and widely varying body of publisher policies regarding data, code, and other supplemental materials. The project team designed this resource to encourage growth and collaboration with other librarians and information professionals facing similar challenges supporting their research communities. This resource creates another access point for researchers to connect with data management services and, as an open-source tool, it can be integrated into the workflows and support services of other libraries.

The DMPTool NIH DMSP Templates Project.

The DMPTool NIH Data Management and Sharing Plan (DMSP) Templates Project was launched in response to the 2023 NIH Data Management and Sharing (DMS) Policy. This new policy introduced a more structured framework for DMS Plans, featuring six key elements, a departure from the 2003 NIH DMS policy. The project aimed to simplify the process for data librarians, research administrators, and researchers by providing a template with curated guidance, eliminating the need to navigate various policies and guidelines. The template breaks out each Plan section and subsection and provides related guidance and examples at the point of need. This effort has resulted in two NIH DMSP Templates. The first is a generic template (NIH-Default) for all ICs, complying with NOT-OD-21-013 and NOT-OD-22-198. More recently, an NIMH-specific template (NIH-NIMH) was added based on NOT-MH-23-100. As of October 2023, over 5,000 DMS Plans have been written using the main NIH-Default template and the NIH-NIMH alternative template.

Searches as data: archiving and sharing search strategies using an institutional data repository.

Background: By defining search strategies and related database exports as code/scripts and data, librarians and information professionals can expand the mandate of research data management (RDM) infrastructure to include this work. This new initiative aimed to create a space in McGill University's institutional data repository for our librarians to deposit and share their search strategies for knowledge syntheses (KS). Case Presentation: The authors, a health sciences librarian and an RDM specialist, created a repository collection of librarian-authored knowledge synthesis (KS) searches in McGill University's Borealis Dataverse collection. We developed and hosted a half-day "Dataverse-a-thon" where we worked with a team of health sciences librarians to develop a standardized KS data management plan (DMP), search reporting documentation, Dataverse software training, and howto guidance for the repository. Conclusion: In addition to better documentation and tracking of KS searches at our institution, the KS Dataverse collection enables sharing of searches among colleagues with discoverable metadata fields for searching within deposited searches. While the initial creation of the DMP and documentation took about six hours, the subsequent deposit of search strategies into the institutional data repository requires minimal effort (e.g., 5-10 minutes on average per deposit). The Dataverse collection also empowers librarians to retain intellectual ownership over search strategies as valuable stand-alone research outputs and raise the visibility of their labor. Overall, institutional data repositories provide specific benefits in facilitating compliance both with PRISMA-S guidance and with RDM best practices.

searchRxiv: A Resource for Sharing Database Search Strategies.

Medical librarians can increase their work visibility and highlight their unique role on evidence synthesis teams with searchRxiv, an open access repository that makes librarian's efforts easily citable and resolves longstanding challenges pertaining to reproducing full search strategies within literature review articles. This column will discuss how to navigate searchRxiv to find, reuse, and cite published search strategies, as well as the process of depositing search strategies.

Setting up a data management infrastructure for bioimaging.

While the FAIR (Findable, Accessible, Interoperable, and Re-usable) principles are well accepted in the scientific community, there are still many challenges in implementing them in the day-to-day scientific process. Data management of microscopy images poses special challenges due to the volume, variety, and many proprietary formats. In particular, appropriate metadata collection, a basic requirement for FAIR data, is a real challenge for scientists due to the technical and content-related aspects. Researchers benefit here from interdisciplinary research network with centralized data management. The typically multimodal structure requires generalized data management and the corresponding acquisition of metadata. Here we report on the establishment of an appropriate infrastructure for the research network by a Core Facility and the development and integration of a software tool MDEmic that allows easy and convenient processing of metadata of microscopy images while providing high flexibility in terms of customization of metadata sets. Since it is also in the interest of the core facility to apply standards regarding the scope and serialization formats to realize successful and sustainable data management for bioimaging, we report on our efforts within the community to define standards in metadata, interfaces, and to reduce the barriers of daily data management.

How Research Data Management Plans Can Help in Harmonizing Open Science and Approaches in the Digital Economy.

Within this perspective article, we intend to summarise definitions and terms that are often used in the context of open science and data-driven R&D and we discuss upcoming European regulations concerning data, data sharing and handling. With this background in hand, we take a closer look at the potential connections and permeable interfaces of open science and digital economy, in which data and resulting immaterial goods can become vital pieces as tradeable items. We believe that both science and the digital economy can profit from a seamless transition and foresee that the scientific outcomes of publicly funded research can be better exploited. To close the gap between open science and the digital economy, and to serve for a balancing of the interests of data producers, data consumers, and an economy around services and the public, we introduce the concept of generic research data management plans (RDMs), which have in part been developed through a community effort and which have been evaluated by academic and industry members of the NFDI4Cat consortium. We are of the opinion that in data-driven research, RDMs do need to become a vital element in publicly funded projects.

Federated electronic data capture (fEDC): Architecture and prototype.

In clinical research as well as patient care, structured documentation of findings is an important task. In many cases, this is achieved by means of electronic case report forms (eCRF) using corresponding information technology systems. To avoid double data entry, eCRF systems can be integrated with electronic health records (EHR). However, when researchers from different institutions collaborate in collecting data, they often use a single joint eCRF system on the Internet. In this case, integration with EHR systems is not possible in most cases due to information security and data protection restrictions. To overcome this shortcoming, we propose a novel architecture for a federated electronic data capture system (fEDC). Four key requirements were identified for fEDC: Definitions of forms have to be available in a reliable and controlled fashion, integration with electronic health record systems must be possible, patient data should be under full local control until they are explicitly transferred for joint analysis, and the system must support data sharing principles accepted by the scientific community for both data model and data captured. With our approach, sites participating in a joint study can run their own instance of an fEDC system that complies with local standards (such as being behind a network firewall) while also being able to benefit from using identical form definitions by sharing metadata in the Operational Data Model (ODM) format published by the Clinical Data Interchange Standards Consortium (CDISC) throughout the collaboration. The fEDC architecture was validated with a working open-source prototype at five German university hospitals. The fEDC architecture provides a novel approach with the potential to significantly improve collaborative data capture: Efforts for data entry are reduced and at the same time, data quality is increased since barriers for integrating with local electronic health record systems are lowered. Further, metadata are shared and patient privacy is ensured at a high level.

Establishing Reliable Research Data Management by Integrating Measurement Devices Utilizing Intelligent Digital Twins.

One of the main topics within research activities is the management of research data. Large amounts of data acquired by heterogeneous scientific devices, sensor systems, measuring equipment, and experimental setups have to be processed and ideally be managed by Findable, Accessible, Interoperable, and Reusable (FAIR) data management approaches in order to preserve their intrinsic value to researchers throughout the entire data lifecycle. The symbiosis of heterogeneous measuring devices, FAIR principles, and digital twin technologies is considered to be ideally suited to realize the foundation of reliable, sustainable, and open research data management. This paper contributes a novel architectural approach for gathering and managing research data aligned with the FAIR principles. A reference implementation as well as a subsequent proof of concept is given, leveraging the utilization of digital twins to overcome common data management issues at equipment-intense research institutes. To facilitate implementation, a top-level knowledge graph has been developed to convey metadata from research devices along with the produced data. In addition, a reactive digital twin implementation of a specific measurement device was devised to facilitate reconfigurability and minimized design effort.

Trends in Research Data Management and Academic Health Sciences Libraries.

Spurred by the National Institute of Health mandating a data management and sharing plan as a requirement of grant funding, research data management has exploded in importance for librarians supporting researchers and research institutions. This editorial examines the role and direction of libraries in this process from several viewpoints. Key markers of success include collaboration, establishing new relationships, leveraging existing relationships, accessing multiple avenues of communication, and building niche expertise and cachè as a valued and trustworthy partner.

The effect of student engagement strategies in online instruction for data management skills.

Evaluating the effectiveness of teaching methods for synchronous online instruction is integral to fostering student engagement and maximizing student learning, particularly in one-time workshops or seminars. Using the lens of social constructivism theory, this study investigated the effect of different approaches of synchronous online instruction on the development of graduate students' research data management (RDM) skills during the post-pandemic era. One experimental group received teacher-centered instruction primarily via lecture and the second experimental group received student-centered instruction with active learning activities. A one-way ANCOVA was used to compare the post-test RDM scores between one control group and the two experimental groups, while controlling for the impact of their pre-test RDM scores. Both experimental groups who received online RDM instruction scored higher than participants from the control group who received no instruction. Additionally, our results indicated that learners who were exposed to more engaged and collaborative instruction demonstrated higher learning outcomes than students who received teacher-centered instruction. These findings suggest that interactive teaching that actively engages the audience is essential for successful synchronous online learning. Simply transferring a lecture-based approach to online teaching will not result in optimal student engagement and learning. The interactive online instructional strategies used in this study (e.g., collective note-taking, Google Jamboard activities) can be applied to any instructional content to engage learners and enhance student learning.

The BMS-LM ontology for biomedical data reporting throughout the lifecycle of a research study: From data model to ontology.

Biomedical research data reuse and sharing is essential for fostering research progress. To this aim, data producers need to master data management and reporting through standard and rich metadata, as encouraged by open data initiatives such as the FAIR (Findable, Accessible, Interoperable, Reusable) guidelines. This helps data re-users to understand and reuse the shared data with confidence. Therefore, dedicated frameworks are required. The provenance reporting throughout a biomedical study lifecycle has been proposed as a way to increase confidence in data while reusing it. The Biomedical Study - Lifecycle Management (BMS-LM) data model has implemented provenance and lifecycle traceability for several multimodal-imaging techniques but this is not enough for data understanding while reusing it. Actually, in the large scope of biomedical research, a multitude of metadata sources, also called Knowledge Organization Systems (KOSs), are available for data annotation. In addition, data producers uses local terminologies or KOSs, containing vernacular terms for data reporting. The result is a set of heterogeneous KOSs (local and published) with different formats and levels of granularity. To manage the inherent heterogeneity, semantic interoperability is encouraged by the Research Data Management (RDM) community. Ontologies, and more specifically top ontologies such as BFO and DOLCE, make explicit the metadata semantics and enhance semantic interoperability. Based on the BMS-LM data model and the BFO top ontology, the BioMedical Study - Lifecycle Management (BMS-LM) core ontology is proposed together with an associated framework for semantic interoperability between heterogeneous KOSs. It is made of four ontological levels: top/core/domain/local and aims to build bridges between local and published KOSs. In this paper, the conversion of the BMS-LM data model to a core ontology is detailed. The implementation of its semantic interoperability in a specific domain context is explained and illustrated with examples from small animal preclinical research.

Digital research data: from analysis of existing standards to a scientific foundation for a modular metadata schema in nanosafety.

BACKGROUND: Assessing the safety of engineered nanomaterials (ENMs) is an interdisciplinary and complex process producing huge amounts of information and data. To make such data and metadata reusable for researchers, manufacturers, and regulatory authorities, there is an urgent need to record and provide this information in a structured, harmonized, and digitized way. RESULTS: This study aimed to identify appropriate description standards and quality criteria for the special use in nanosafety. There are many existing standards and guidelines designed for collecting data and metadata, ranging from regulatory guidelines to specific databases. Most of them are incomplete or not specifically designed for ENM research. However, by merging the content of several existing standards and guidelines, a basic catalogue of descriptive information and quality criteria was generated. In an iterative process, our interdisciplinary team identified deficits and added missing information into a comprehensive schema. Subsequently, this overview was externally evaluated by a panel of experts during a workshop. This whole process resulted in a minimum information table (MIT), specifying necessary minimum information to be provided along with experimental results on effects of ENMs in the biological context in a flexible and modular manner. The MIT is divided into six modules: general information, material information, biological model information, exposure information, endpoint read out information and analysis and statistics. These modules are further partitioned into module subdivisions serving to include more detailed information. A comparison with existing ontologies, which also aim to electronically collect data and metadata on nanosafety studies, showed that the newly developed MIT exhibits a higher level of detail compared to those existing schemas, making it more usable to prevent gaps in the communication of information. CONCLUSION: Implementing the requirements of the MIT into e.g., electronic lab notebooks (ELNs) would make the collection of all necessary data and metadata a daily routine and thereby would improve the reproducibility and reusability of experiments. Furthermore, this approach is particularly beneficial regarding the rapidly expanding developments and applications of novel non-animal alternative testing methods.

Characterizing the research data management practices of NIH biomedical researchers indicates the need for better support at laboratory level.

BACKGROUND: The study investigated the research data management (RDM) practices of biomedical researchers at the National Institutes of Health (NIH) representing various biomedical disciplines. OBJECTIVES: This study aimed to analyse the state of biomedical researchers' RDM practices based on RDM practice levels (individual, laboratory, institution and external). The findings of the study are expected to provide directions to information professionals for effective RDM services. METHODS: Semi-structured interviews with 11 researchers were conducted. The interviews were analysed by levels of RDM practices. RESULTS: The findings revealed that biomedical researchers focus on storing and sharing data and that RDM is performed mainly at the individual level. There seems to be a lack of laboratory level RDM system that allows consistent RDM practices among researchers. External RDM practice is often challenged by not having one responsible for RDM. DISCUSSION: Findings suggested a need for an agreed RDM system and customized support, particularly at the laboratory level. Also, institutional support can help researchers prepare for long term data preservation. CONCLUSION: Our suggestions emphasize the importance of RDM training and support for long term data preservation, especially at the laboratory level.

Transforming and extending library services by embracing technology and collaborations: A case study.

Technology advances and collaborations with information technology and computer science groups have enabled library services to expand into new domains. Listening to user needs, eliminating administrative burden and saving users time remain strong foundations on which to build new library services enabled by technology. Examples of what is now possible is described, including service to user groups, successes, failures and challenges. Although technology advances have enabled library service enhancements to all user groups, special emphasis on new library services in support of the research enterprise is discussed. As Lindberg and Humphreys predicted in 2015, the research enterprise's need for responsible curation of research data has created new opportunities for library services and examples of those services are discussed. As technology continues to advance, new library services are expected to emerge. These may include regulatory and compliance services. By developing these services with user feedback to save users time and expedite their work, and in collaboration with technology experts, libraries can expect to offer sustainable and valued services for years to come.

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices.

Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.

Effectiveness of data auditing as a tool to reinforce good research data management (RDM) practice: a Singapore study.

BACKGROUND: Institutions, funding agencies and publishers are placing increasing emphasis on good research data management (RDM). RDM lapses in medical science can result in questionable data and cause the public's confidence in the scientific community to crumble. A fledgling medical school in a young university in Singapore has mandated every funded research project to have a data management plan (DMP). However, researchers' adherence to their DMPs was unknown until the school embarked on routine data auditing. We hypothesize that research data auditing improves RDM awareness, compliance and reception in the school. METHODS: We conducted surveys with research PIs and researchers before and after data auditing to evaluate differences in self-reported RDM awareness, compliance and reception. As it is mandatory to deposit research data in a central data repository system in the school, we tracked data deposition by each laboratory from 2 weeks before to 3 months after data auditing as a marker of actual RDM compliance. RESULTS: Research data auditing had an overall positive effect on self-reported RDM awareness, compliance and reception for both research PIs and researchers. Research PIs agreed more that RDM was important to scientific reproducibility, were more aware of proper RDM, had higher RDM strength in their laboratories and were more compliant with the DMP. Both research PIs and researchers believed data auditing helped them to be more compliant with data deposition in the repository. However, data auditing had no significant impact on laboratories' data deposition rates over time, which could be due to the short sampling period. CONCLUSIONS: Research PIs and researchers generally felt that data auditing was effective in improving RDM practices. It helped to evaluate their RDM practices objectively, propose corrective actions for RDM lapses and spread awareness of the university's data management policies. Our findings corroborated other studies in medical research, geosciences, engineering and ethics that data auditing promotes good RDM practices. Hence, we recommend research institutions worldwide to adopt data auditing as a tool to reinforce research integrity.

Requirements and Operational Guidelines for Secure and Sustainable Digital Phenotyping: Design and Development Study.

BACKGROUND: Digital phenotyping, the measurement of human behavioral phenotypes using personal devices, is rapidly gaining popularity. Novel initiatives, ranging from software prototypes to user-ready research platforms, are innovating the field of biomedical research and health care apps. One example is the BEHAPP project, which offers a fully managed digital phenotyping platform as a service. The innovative potential of digital phenotyping strategies resides among others in their capacity to objectively capture measurable and quantitative components of human behavior, such as diurnal rhythm, movement patterns, and communication, in a real-world setting. The rapid development of this field underscores the importance of reliability and safety of the platforms on which these novel tools are operated. Large-scale studies and regulated research spaces (eg, the pharmaceutical industry) have strict requirements for the software-based solutions they use. Security and sustainability are key to ensuring continuity and trust. However, the majority of behavioral monitoring initiatives have not originated primarily in these regulated research spaces, which may be why these components have been somewhat overlooked, impeding the further development and implementation of such platforms in a secure and sustainable way. OBJECTIVE: This study aims to provide a primer on the requirements and operational guidelines for the development and operation of a secure behavioral monitoring platform. METHODS: We draw from disciplines such as privacy law, information, and computer science to identify a set of requirements and operational guidelines focused on security and sustainability. Taken together, the requirements and guidelines form the foundation of the design and implementation of the BEHAPP behavioral monitoring platform. RESULTS: We present the base BEHAPP data collection and analysis flow and explain how the various concepts from security and sustainability are addressed in the design. CONCLUSIONS: Digital phenotyping initiatives are steadily maturing. This study helps the field and surrounding stakeholders to reflect upon and progress toward secure and sustainable operation of digital phenotyping-driven research.