Findable, Accessible, Interoperable And Reusable Research Articles

The Role of the European Reference Network for Rare Bone Diseases (ERN BOND) and European Registries for Rare Bone and Mineral Conditions (EuRR-Bone) in the Governance of the Management of Rare Bone and Mineral Diseases.

Rare diseases (RDs) bear a significant challenge to individuals, healthcare systems, and societies. The European reference network on Rare BONe diseases (ERN BOND) is committed to improving multidisciplinary, patient-centred care for individuals with rare bone and mineral diseases (RBMDs). Its affiliated project, the European registries for rare bone and mineral conditions (EuRR-Bone) collects data using two different platforms, an electronic surveillance system (e-REC) that captures the occurrence of RBMDs and the Core Registry, a platform with the infrastructure for collecting Core data fields and longitudinal generic and condition-specific information. With emerging registries and the overlap with other ERNs, it is key to maintain the capability of the platforms to adapt to the needs of the network and the community whilst adhering to quality and FAIR (findable, accessible, interoperable, and reusable) principles. This binomial ensures long-term sustainability and potential advances in the care pathway of RBMDs whilst promoting good practice standards within Europe and beyond.

FAIRsoft-A practical implementation of FAIR principles for research software.

Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, contain unknown errors that affect the outcome, or be directly unavailable and impossible to use for others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (Findable, Accessible, Interoperable, and Reusable) Data Principles. We present here a comprehensive series of quantitative indicators based on a pragmatic interpretation of the FAIR Principles and their implementation on OpenEBench, ELIXIR's open platform providing both support for scientific benchmarking and an active observatory of quality-related features for Life Sciences research software. The results serve to understand the current practices around research software quality-related features and provide objective indications for improving them. Software metadata, from 11 different sources, collected, integrated and analysed in the context of this manuscript are available at https://doi.org/10.5281/zenodo.7311067. Code used for software metadata retrieval and processing is available in the following repository https://gitlab.bsc.es/inb/elixir/software-observatory/FAIRsoft_ETL. Supplementary data are available at Bioinformatics online.

Toward a community model of scholarly editing: FAIR/CARE, research ethics, & labour visibility

Historically, scholarly editions of music have identified a managing editor and individual volume editors. Other contributors might receive an acknowledgement with a vague description of activities, with institutional support often appearing in the printed metadata. This model’s emphasis on single scholars perpetuates a myth, relying heretofore upon predominantly invisible labour. Digital editions require interdisciplinary collaboration combining musicological skills, technical skills, and infrastructural resources, thus challenging this model’s ability to endure. Moreover, digital editions proffer opportunities for reconsidering the roles, workflows, and knowledge structures involved in critical musical scholarship. Situated at the intersection of currently running and recently completed digital projects, continuously emergent tools, sociology, and philosophy, this essay reflects on the role of the editor in the digital age. Beginning with Howard Becker’s art worlds model of creative communities, it suggests a model based on FAIR (Findable, Accessible, Interoperable, and Reusable) and CARE (Collective Benefit, Authority to Control, Responsibility, and Ethics) principles and the Music Encoding Initiative (MEI). MEI affords expansive metadata recording for contributors – composers, librettists, performers, editors, researchers, funders, etc. – to a work and its embodiments, which in turn enables broader visibility and empowers greater acknowledgement of the labour involved in such projects. Alongside other digital projects, this essay pays particular attention to how these technological and team-focused concepts are at- and in-play in the Reger-Werkausgabe Online.

Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets

To explore complex biological questions, it is often necessary to access various data types from public data repositories. As the volume and complexity of biological sequence data grow, public repositories face significant challenges in ensuring that the data is easily discoverable and usable by the biological research community. To address these challenges, the National Center for Biotechnology Information (NCBI) has created NCBI Datasets. This resource provides straightforward, comprehensive, and scalable access to biological sequences, annotations, and metadata for a wide range of taxa. Following the FAIR (Findable, Accessible, Interoperable, and Reusable) data management principles, NCBI Datasets offers user-friendly web interfaces, command-line tools, and documented APIs, empowering researchers to access NCBI data seamlessly. The data is delivered as packages of sequences and metadata, thus facilitating improved data retrieval, sharing, and usability in research. Moreover, this data delivery method fosters effective data attribution and promotes its further reuse. This paper outlines the current scope of data accessible through NCBI Datasets and explains various options for exploring and downloading the data.

European Health Information Portal: a one-stop shop for health information.

Timely and high-quality population-level health information is needed to support evidence-informed decision-making, for planning and evaluation of prevention, care and cure activities as well as for research to generate new knowledge. FAIR (Findable, Accessible, Interoperable and Reusable) principles are one of the key elements supporting health research and making it more cost-effective through the reuse of already existing data. Currently, health data are in many countries dispersed and difficult to find and access. Two EU Public Health Programmes co-funded Joint Actions, Information for Action (InfAct) and Population Health Information Research Infrastructure (PHIRI) have established a European Health Information Portal, a web-based service, to facilitate better findability, access, interoperability and reuse of existing health information. The European Health Information Portal (www.healthinformationportal.eu) has been established including sections on National Nodes, data sources, publications, health information projects within countries and across Europe, research networks and research infrastructures, ethical and legal issues for health information exchange and use, capacity-building activities in all areas of population health and a dedicated COVID-19 section. The European Health Information Portal, being a central place for a wide range of population health information from EU Member States, is an information source for researchers, policy-makers and other relevant stakeholders. It is important to ensure the sustainability of the portal, especially in light of the European Health Data Space (EHDS) Regulation proposal and its requirements regarding the secondary use of health data.

Operationalizing and digitizing person-centered daily functioning: a case for functionomics

An ever-increasing amount of data on a person’s daily functioning is being collected, which holds information to revolutionize person-centered healthcare. However, the full potential of data on daily functioning cannot yet be exploited as it is mostly stored in an unstructured and inaccessible manner. The integration of these data, and thereby expedited knowledge discovery, is possible by the introduction of functionomics as a complementary ‘omics’ initiative, embracing the advances in data science. Functionomics is the study of high-throughput data on a person’s daily functioning, that can be operationalized with the International Classification of Functioning, Disability and Health (ICF).A prerequisite for making functionomics operational are the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This paper illustrates a step by step application of the FAIR principles for making functionomics data machine readable and accessible, under strictly certified conditions, in a practical example. Establishing more FAIR functionomics data repositories, analyzed using a federated data infrastructure, enables new knowledge generation to improve health and person-centered healthcare. Together, as one allied health and healthcare research community, we need to consider to take up the here proposed methods.

A data integration framework of additive manufacturing based on FAIR principles

Laser-powder bed fusion (L-PBF) is a popular additive manufacturing (AM) process with rich data sets coming from both in situ and ex situ sources. Data derived from multiple measurement modalities in an AM process capture unique features but often have different encoding methods; the challenge of data registration is not directly intuitive. In this work, we address the challenge of data registration between multiple modalities. Large data spaces must be organized in a machine-compatible method to maximize scientific output. FAIR (findable, accessible, interoperable, and reusable) principles are required to overcome challenges associated with data at various scales. FAIRified data enables a standardized format allowing for opportunities to generate automated extraction methods and scalability. We establish a framework that captures and integrates data from a L-PBF study such as radiography and high-speed camera video, linking these data sets cohesively allowing for future exploration.Graphical abstract

Best practices for genetic and genomic data archiving.

Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.

Building an open-source collaborative platform for migration research: A metadata modeling approach using XML

Public access to well-organized migration data repositories is rare. While open migration data are available, most are dispersed, challenging their organization. This work uses a metadata modeling approach to organize migration-related data and research components hosted in an open-source, collaborative research environment. The proposed platform integrates data, computational models, application libraries, and research projects in a unified environment for research. An overview of the metadata modeling process and the XML technology used to integrate the platform components was provided, along with descriptions of the platform’s essential features, such as standardized exchange of information for data organization and sharing and collaborative authoring. The design of a prototype collaborative, open-source migration data and modeling research platform using sample data and software components was built and hosted on GitHub for testing and refinement purposes. It allows the authors to collaborate, improve, and assess the platform’s functionalities and capabilities. Our platform, COSMOS (Collaborative Open-Source Modeling System), adopted the creation and use of open data formats for alignment with FAIR (Findable, Accessible, Interoperable, and Reusable) data principles to ensure that data at the prototype level is consistent with and can be used by the international migration research community in the future. By providing a standardized framework for data organization, data sharing, and collaboration, the platform can help accelerate scientific discovery and advance our understanding of complex social and cultural phenomena such as immigration.

A novel digitalization approach for smart materials – ontology‐based access to data and models

Smart materials react to physical fields (e.g. electric, magnetic and thermal fields) and can be used as sensors, actuators and generators due to their bidirectional behavior. Easy and multiscale access to material data and models enables efficient research and development with regard to the selection of appropriate materials and their optimization towards specific applications. However, different working principles, measurement and analysis methods, as well as data storage approaches lead to heterogeneous and partly inconsistent datasets. The ontology‐based data access (OBDA) is a suitable method to access such heterogeneous datasets easily and quickly, while material models can transform material data across certain scales for different applications. In order to connect both capabilities, we present an extended approach enabling an ontology‐based data and model access (OBDMA), also supporting FAIR (Findable, Accessible, Interoperable, and Re‐usable). The OBDMA system comprises four main levels, the query, the ontology, the mapping and the database. Storing knowledge at these different levels increases the interchangeability and enables variable datasets, which is essential, especially for dynamic research fields such as smart materials. In our paper, the principles and advantages of the OBDMA approach are demonstrated for different subclasses of smart materials, but can be transferred to other materials, too.This article is protected by copyright. All rights reserved.

A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials.

Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.

A practical guide to data management and sharing for biomedical laboratory researchers

Effective data management and sharing have become increasingly crucial in biomedical research; however, many laboratory researchers lack the necessary tools and knowledge to address this challenge. This article provides an introductory guide into research data management (RDM), and the importance of FAIR (Findable, Accessible, Interoperable, and Reusable) data-sharing principles for laboratory researchers produced by practicing scientists. We explore the advantages of implementing organized data management strategies and introduce key concepts such as data standards, data documentation, and the distinction between machine and human-readable data formats. Furthermore, we offer practical guidance for creating a data management plan and establishing efficient data workflows within the laboratory setting, suitable for labs of all sizes. This includes an examination of requirements analysis, the development of a data dictionary for routine data elements, the implementation of unique subject identifiers, and the formulation of standard operating procedures (SOPs) for seamless data flow. To aid researchers in implementing these practices, we present a simple organizational system as an illustrative example, which can be tailored to suit individual needs and research requirements.By presenting a user-friendly approach, this guide serves as an introduction to the field of RDM and offers practical tips to help researchers effortlessly meet the common data management and sharing mandates rapidly becoming prevalent in biomedical research.

InChI isotopologue and isotopomer specifications

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically-resolved chemical entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically-resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry.Scientific contributionThis new extension to the InChI standard would enable improved annotation of analytical datasets characterizing chemical entities, supporting the FAIR (Findable, Accessible, Interoperable, and Reusable) guiding principles of data stewardship for chemical datasets, ultimately promoting Open Science in chemistry.

Colorectal cancer health and care quality indicators in a federated setting using the Personal Health Train

ObjectiveHospitals and healthcare providers should assess and compare the quality of care given to patients and based on this improve the care. In the Netherlands, hospitals provide data to national quality registries, which in return provide annual quality indicators. However, this process is time-consuming, resource intensive and risks patient privacy and confidentiality. In this paper, we presented a multicentric ‘Proof of Principle’ study for federated calculation of quality indicators in patients with colorectal cancer. The findings suggest that the proposed approach is highly time-efficient and consume significantly lesser resources.Materials and methodsTwo quality indicators are calculated in an efficient and privacy presevering federated manner, by i) applying the Findable Accessible Interoperable and Reusable (FAIR) data principles and ii) using the Personal Health Train (PHT) infrastructure. Instead of sharing data to a centralized registry, PHT enables analysis by sending algorithms and sharing only insights from the data.ResultsETL process extracted data from the Electronic Health Record systems of the hospitals, converted them to FAIR data and hosted in RDF endpoints within each hospital. Finally, quality indicators from each center are calculated using PHT and the mean result along with the individual results plotted.Discussion and conclusionPHT and FAIR data principles can efficiently calculate quality indicators in a privacy-preserving federated approach and the work can be scaled up both nationally and internationally. Despite this, application of the methodology was largely hampered by ELSI issues. However, the lessons learned from this study can provide other hospitals and researchers to adapt to the process easily and take effective measures in building quality of care infrastructures.

Bayesian modelling of time series data (BayModTS)-a FAIR workflow to process sparse and highly variable data.

Systems biology aims to better understand living systems through mathematical modelling of experimental and clinical data. A pervasive challenge in quantitative dynamical modelling is the integration of time series measurements, which often have high variability and low sampling resolution. Approaches are required to utilize such information while consistently handling uncertainties. We present BayModTS (Bayesian modelling of time series data), a new FAIR (findable, accessible, interoperable, and reusable) workflow for processing and analysing sparse and highly variable time series data. BayModTS consistently transfers uncertainties from data to model predictions, including process knowledge via parameterized models. Further, credible differences in the dynamics of different conditions can be identified by filtering noise. To demonstrate the power and versatility of BayModTS, we applied it to three hepatic datasets gathered from three different species and with different measurement techniques: (i) blood perfusion measurements by magnetic resonance imaging in rat livers after portal vein ligation, (ii) pharmacokinetic time series of different drugs in normal and steatotic mice, and (iii) CT-based volumetric assessment of human liver remnants after clinical liver resection. The BayModTS codebase is available on GitHub at https://github.com/Systems-Theory-in-Systems-Biology/BayModTS. The repository contains a Python script for the executable BayModTS workflow and a widely applicable SBML (systems biology markup language) model for retarded transient functions. In addition, all examples from the paper are included in the repository. Data and code of the application examples are stored on DaRUS: https://doi.org/10.18419/darus-3876. The raw MRI ROI voxel data were uploaded to DaRUS: https://doi.org/10.18419/darus-3878. The steatosis metabolite data are published on FairdomHub: 10.15490/fairdomhub.1.study.1070.1.

Model-Driven Approach for Making Citizen Science Data FAIR

Citizen Science (CS) initiatives have proliferated in different scientific and social fields, producing vast amounts of data. Existing CS projects usually adopt PPSR Core as a data and metadata standard. However, these projects are still not FAIR (Findable, Accessible, Interoperable and Reusable)-compliant. We propose to use DCAT as a data and metadata standard since it helps to improve the interoperability of CS data catalogs and all the FAIR features. For this purpose, in this paper we present a model-driven approach to make CS data FAIR. Our approach has the following contributions: (i) the definition of a metamodel based on PPSR Core, (ii) the definition of a DCAT profile for CS, (iii) a definition of set of automated transformations from PPSR Core to DCAT. Finally, the implementation of the model-driven process has been validated by evaluating several FAIR metrics. The results show that our proposal has significantly improved the FAIR quality of CS projects.

Resurrecting, reinterpreting and reusing stratigraphy: an afterlife for archaeological data

Stratigraphic data form the backbone of archaeological records from excavated sites and are essential for the integrated analysis and wider interpretation of artefacts and sites. Accessible archiving of this data is therefore vital for understanding and revisiting such interpretations. Here, the authors highlight the need for more consistent digital records of stratigraphic and associated temporal relationships derived during post-excavation analysis phasing activities. They argue for the distillation of best practice in post-excavation procedures and the application of consistent and persistent terminology to make this fundamental archaeological data sustainably FAIR (findable, accessible, interoperable and reusable) and ‘Open’ across present-day geopolitical and spatiotemporal boundaries.

Brainlife.io: a decentralized and open-source cloud platform to support neuroscience research

Neuroscience is advancing standardization and tool development to support rigor and transparency. Consequently, data pipeline complexity has increased, hindering FAIR (findable, accessible, interoperable and reusable) access. brainlife.io was developed to democratize neuroimaging research. The platform provides data standardization, management, visualization and processing and automatically tracks the provenance history of thousands of data objects. Here, brainlife.io is described and evaluated for validity, reliability, reproducibility, replicability and scientific utility using four data modalities and 3,200 participants.

An open source knowledge graph ecosystem for the life sciences.

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoint resources and abstraction algorithms), and benchmarks (e.g., prebuilt KGs). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 different large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

Semantics-Enabled Data Federation: Bringing Materials Scientists Closer to FAIR Data

The development and discovery of new materials can be significantly enhanced through the adoption of FAIR (Findable, Accessible, Interoperable, and Reusable) data principles and the establishment of a robust data infrastructure in support of materials informatics. A FAIR data infrastructure and associated best practices empower materials scientists to access and make the most of a wealth of information on materials properties, structures, and behaviors, allowing them to collaborate effectively, and enable data-driven approaches to material discovery. To make data findable, accessible, interoperable, and reusable to materials scientists, we developed and are in the process of expanding a materials data infrastructure to capture, store, and link data to enable a variety of analytics and visualizations. Our infrastructure follows three key architectural design philosophies: (i) capture data across a federated storage layer to minimize the storage footprint and maximize the query performance for each data type, (ii) use a knowledge graph-based data fusion layer to provide a single logical interface above the federated data repositories, and (iii) provide an ensemble of FAIR data access and reuse services atop the knowledge graph to make it easy for materials scientists and other domain experts to explore, use, and derive value from the data. This paper details our architectural approach, open-source technologies used to build the capabilities and services, and describes two applications through which we have successfully demonstrated its use. In the first use case, we created a system to enable additive manufacturing data storage and process parameter optimization with a range of user-friendly visualizations. In the second use case, we created a system for exploring data from cathodic arc deposition experiments to develop a new steam turbine coating material, fusing a combination of materials data with physics-based equations to enable advanced reasoning over the combined knowledge using a natural language chatbot-like user interface.