Findable, Accessible, Interoperable, Reusable Research Articles

Research data management for bioimaging: the 2021 NFDI4BIOIMAGE community survey.

Background Knowing the needs of the bioimaging community with respect to research data management (RDM) is essential for identifying measures that enable adoption of the FAIR (findable, accessible, interoperable, reusable) principles for microscopy and bioimage analysis data across disciplines. As an initiative within Germany's National Research Data Infrastructure, we conducted this community survey in summer 2021 to assess the state of the art of bioimaging RDM and the community needs. Methods An online survey was conducted with a mixed question-type design. We created a questionnaire tailored to relevant topics of the bioimaging community, including specific questions on bioimaging methods and bioimage analysis, as well as more general questions on RDM principles and tools. 203 survey entries were included in the analysis covering the perspectives from various life and biomedical science disciplines and from participants at different career levels. Results The results highlight the importance and value of bioimaging RDM and data sharing. However, the practical implementation of FAIR practices is impeded by technical hurdles, lack of knowledge, and insecurity about the legal aspects of data sharing. The survey participants request metadata guidelines and annotation tools and endorse the usage of image data management platforms. At present, OMERO (Open Microscopy Environment Remote Objects) is the best known and most widely used platform. Most respondents rely on image processing and analysis, which they regard as the most time-consuming step of the bioimage data workflow. While knowledge about and implementation of electronic lab notebooks and data management plans is limited, respondents acknowledge their potential value for data handling and publication. Conclusions The bioimaging community acknowledges and endorses the value of RDM and data sharing. Still, there is a need for information, guidance, and standardization to foster the adoption of FAIR data handling. This survey may help inspiring targeted measures to close this gap.

FAIR and Interactive Data Graphics from a Scientific Knowledge Graph

Graph databases capture richly linked domain knowledge by integrating heterogeneous data and metadata into a unified representation. Here, we present the use of bespoke, interactive data graphics (bar charts, scatter plots, etc.) for visual exploration of a knowledge graph. By modeling a chart as a set of metadata that describes semantic context (SPARQL query) separately from visual context (Vega-Lite specification), we leverage the high-level, declarative nature of the SPARQL and Vega-Lite grammars to concisely specify web-based, interactive data graphics synchronized to a knowledge graph. Resources with dereferenceable URIs (uniform resource identifiers) can employ the hyperlink encoding channel or image marks in Vega-Lite to amplify the information content of a given data graphic, and published charts populate a browsable gallery of the database. We discuss design considerations that arise in relation to portability, persistence, and performance. Altogether, this pairing of SPARQL and Vega-Lite—demonstrated here in the domain of polymer nanocomposite materials science—offers an extensible approach to FAIR (findable, accessible, interoperable, reusable) scientific data visualization within a knowledge graph framework.

The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics-How Can Research and Development Benefit?

Recently, CEN/TS 17626:2021, the European pre-analytical standard for human specimens intended for microbiome DNA analysis, was published. Although this standard relates to diagnostic procedures for microbiome analysis and is relevant for in vitro diagnostic (IVD) manufacturers and diagnostic laboratories, it also has implications for research and development (R&D). We present here why standards are needed in biomedical research, what pre-analytical standards can accomplish, and which elements of the pre-analytical workflow they cover. The benefits of standardization for the generation of FAIR (findable, accessible, interoperable, reusable) data and to support innovation are briefly discussed.

Adamant: a JSON schema-based metadata editor for research data management workflows.

The web tool Adamant has been developed to systematically collect research metadata as early as the conception of the experiment. Adamant enables a continuous, consistent, and transparent research data management (RDM) process, which is a key element of good scientific practice ensuring the path to Findable, Accessible, Interoperable, Reusable (FAIR) research data. It simplifies the creation of on-demand metadata schemas and the collection of metadata according to established or new standards. The approach is based on JavaScript Object Notation (JSON) schema, where any valid schema can be presented as an interactive web-form. Furthermore, Adamant eases the integration of numerous available RDM methods and software tools into the everyday research activities of especially small independent laboratories. A programming interface allows programmatic integration with other software tools such as electronic lab books or repositories. The user interface (UI) of Adamant is designed to be as user friendly as possible. Each UI element is self-explanatory and intuitive to use, which makes it accessible for users that have little to no experience with JSON format and programming in general. Several examples of research data management workflows that can be implemented using Adamant are introduced. Adamant (client-only version) is available from: https://plasma-mds.github.io/adamant.

Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database.

Improving the understanding of the oligogenic nature of diseases requires access to high-quality, well-curated Findable, Accessible, Interoperable, Reusable (FAIR) data. Although first steps were taken with the development of the Digenic Diseases Database, leading to novel computational advancements to assist the field, these were also linked with a number of limitations, for instance, the ad hoc curation protocol and the inclusion of only digenic cases. The OLIgogenic diseases DAtabase (OLIDA) presents a novel, transparent and rigorous curation protocol, introducing a confidence scoring mechanism for the published oligogenic literature. The application of this protocol on the oligogenic literature generated a new repository containing 916 oligogenic variant combinations linked to 159 distinct diseases. Information extracted from the scientific literature is supplemented with current knowledge support obtained from public databases. Each entry is an oligogenic combination linked to a disease, labelled with a confidence score based on the level of genetic and functional evidence that supports its involvement in this disease. These scores allow users to assess the relevance and proof of pathogenicity of each oligogenic combination in the database, constituting markers for reporting improvements on disease-causing oligogenic variant combinations. OLIDA follows the FAIR principles, providing detailed documentation, easy data access through its application programming interface and website, use of unique identifiers and links to existing ontologies.Database URL https://olida.ibsquare.be

Transparency in quality of radiotherapy for breast cancer in the Netherlands: a national registration of radiotherapy-parameters

BackgroundRadiotherapy (RT) is part of the curative treatment of approximately 70% of breast cancer (BC) patients. Wide practice variation has been reported in RT dose, fractionation and its treatment planning for BC. To decrease this practice variation, it is essential to first gain insight into the current variation in RT treatment between institutes. This paper describes the development of the NABON Breast Cancer Audit-Radiotherapy (NBCA-R), a structural nationwide registry of BC RT data of all BC patients treated with at least surgery and RT.MethodsA working group consisting of representatives of the BC Platform of the Dutch Radiotherapy Society selected a set of dose volume parameters deemed to be surrogate outcome parameters, both for tumour control and toxicity. Two pilot studies were carried out in six RT institutes. In the first pilot study, data were manually entered into a secured web-based system. In the second pilot study, an automatic Digital Imaging and Communications in Medicine (DICOM) RT upload module was created and tested.ResultsThe NBCA-R dataset was created by selecting RT parameters describing given dose, target volumes, coverage and homogeneity, and dose to organs at risk (OAR). Entering the data was made mandatory for all Dutch RT departments. In the first pilot study (N = 1093), quite some variation was already detected. Application of partial breast irradiation varied from 0 to 17% between the 6 institutes and boost to the tumour bed from 26.5 to 70.2%. For patients treated to the left breast or chest wall only, the average mean heart dose (MHD) varied from 0.80 to 1.82 Gy; for patients treated to the breast/chest wall only, the average mean lung dose (MLD) varied from 2.06 to 3.3 Gy. In the second pilot study 6 departments implemented the DICOM-RT upload module in daily practice. Anonymised data will be available for researchers via a FAIR (Findable, Accessible, Interoperable, Reusable) framework.ConclusionsWe have developed a set of RT parameters and implemented registration for all Dutch BC patients. With the use of an automated upload module registration burden will be minimized. Based on the data in the NBCA-R analyses of the practice variation will be done, with the ultimate aim to improve quality of BC RT.Trial registration Retrospectively registered.

Emacs as a Tool for Modern Science

It is human nature to prefer additive problem solving even if removal may be the more efficient solution. This heuristic has wide ranging implications when dealing with science, innovation and complex problem solving. This is compounded when dealing with these issues at an institutional level. Additive solutions to workflows with extra software tools and proprietary digital solutions can impede work without offering any advantages in terms of Findable, Accessible, Interoperable, Reusable (FAIR) data principles or productivity. This viewpoint highlights one possible workflow and the mentality underpinning it with an aim to incorporate FAIR data, improved productivity and longevity of written documents while improving workloads within industrial research and development (R&D).

On the reproducibility of enzyme reactions and kinetic modelling.

Enzyme reactions are highly dependent on reaction conditions. To ensure reproducibility of enzyme reaction parameters, experiments need to be carefully designed and kinetic modeling meticulously executed. Furthermore, to enable quality control of enzyme reaction parameters, the experimental conditions, the modeling process as well as the raw data need to be reported comprehensively. By taking these steps, enzyme reaction parameters can be open and FAIR (findable, accessible, interoperable, re-usable) as well as repeatable, replicable and reproducible. This review discusses these requirements and provides a practical guide to designing initial rate experiments for the determination of enzyme reaction parameters and gives an open, FAIR and re-editable example of the kinetic modeling of an enzyme reaction. Both the guide and example are scripted with Python in Jupyter Notebooks and are publicly available (https://fairdomhub.org/investigations/483/snapshots/1). Finally, the prerequisites of automated data analysis and machine learning algorithms are briefly discussed to provide further motivation for the comprehensive, open and FAIR reporting of enzyme reaction parameters.

From FAIR to FAIRS: Data security by design for the global burden of animal diseases.

Solving complex global problems involving data and data analysis can require data from both the public and private sectors. The sharing of data has traditionally been restricted to open data. To facilitate the use of both open and private data, a new data-sharing framework has been constructed as an extension to the popular Findable-Accessible-Interoperable-Reusable (FAIR) framework. The "Secure by Design" approach has been taken to define the FAIRS data-sharing framework where S stands for Secure. A Cloud infrastructure architecture is proposed that would allow data brokers to implement FAIRS. This architecture is being constructed for the Global Burden of Animal Diseases (GBADs) to facilitate the sharing of livestock data.

Paths towards greater consensus building in experimental biology.

In a recent editorial, the Editors-in-Chief of Journal of Experimental Biology argued that consensus building, data sharing, and better integration across disciplines are needed to address the urgent scientific challenges posed by climate change. We agree and expand on the importance of cross-disciplinary integration and transparency to improve consensus building and advance climate change research in experimental biology. We investigated reproducible research practices in experimental biology through a review of open data and analysis code associated with empirical studies on three debated paradigms and for unrelated studies published in leading journals in comparative physiology and behavioural ecology over the last 10 years. Nineteen per cent of studies on the three paradigms had open data, and 3.2% had open code. Similarly, 12.1% of studies in the journals we examined had open data, and 3.1% had open code. Previous research indicates that only 50% of shared datasets are complete and re-usable, suggesting that fewer than 10% of studies in experimental biology have usable open data. Encouragingly, our results indicate that reproducible research practices are increasing over time, with data sharing rates in some journals reaching 75% in recent years. Rigorous empirical research in experimental biology is key to understanding the mechanisms by which climate change affects organisms, and ultimately promotes evidence-based conservation policy and practice. We argue that a greater adoption of open science practices, with a particular focus on FAIR (Findable, Accessible, Interoperable, Re-usable) data and code, represents a much-needed paradigm shift towards improved transparency, cross-disciplinary integration, and consensus building to maximize the contributions of experimental biologists in addressing the impacts of environmental change on living organisms.

AccTEF: A Transparency and Accountability Evaluation Framework for Ontology-Based Systems

This paper proposes a new accountability and transparency evaluation framework (AccTEF) for ontology-based systems (OSysts). AccTEF is based on an analysis of the relation between a set of widely accepted data governance principles, i.e. findable, accessible, interoperable, reusable (FAIR) and accountability and transparency concepts. The evaluation of accountability and transparency of input ontologies and vocabularies of OSysts are addressed by analyzing the relation between vocabulary and ontology quality evaluation metrics, FAIR and accountability and transparency concepts. An ontology-based knowledge extraction pipeline is used as a use case in this study. Discovering the relation between FAIR and accountability and transparency helps in identifying and mitigating risks associated with deploying OSysts. This also allows providing design guidelines that help accountability and transparency to be embedded in OSysts. We found that FAIR can be used as a transparency indicator. We also found that the studied vocabulary and ontology quality evaluation metrics do not cover FAIR, accountability and transparency. Accordingly, we suggest these concepts should be considered as vocabulary and ontology quality evaluation aspects. To the best of our knowledge, it is the first time that the relation between FAIR and accountability and transparency concepts has been found and used for evaluation.

AusGeochem: An Open Platform for Geochemical Data Preservation, Dissemination and Synthesis

To promote a more efficient and transparent geochemistry data ecosystem, a consortium of Australian university research laboratories called the AuScope Geochemistry Network assembled to build a collaborative platform for the express purpose of preserving, disseminating and collating geochronology and isotopic data. In partnership with geoscience‐data‐solutions company Lithodat Pty Ltd, the open, cloud‐based AusGeochem platform (https://ausgeochem.auscope.org.au) was developed to simultaneously serve as a geosample registry, a geochemical data repository and a data analysis tool. Informed by method‐specific groups of geochemistry experts and established international data reporting practices, community‐agreed database schemas were developed for rock and mineral geosample metadata and secondary ion mass spectrometry U‐Pb analysis, with additional models for laser ablation‐inductively coupled‐mass spectrometry U‐Pb and Lu‐Hf, Ar‐Ar, fission‐track and (U‐Th‐Sm)/He under development. Collectively, the AusGeochem platform provides the geochemistry community with a new, dynamic resource to help facilitate FAIR (Findable, Accessible, Interoperable, Reusable) data management, streamline data dissemination and advanced quantitative investigations of Earth system processes. By systematically archiving detailed geochemical (meta‐)data in structured schemas, intractably large datasets comprising thousands of analyses produced by numerous laboratories can be readily interrogated in novel and powerful ways. These include rapid derivation of inter‐data relationships, facilitating on‐the‐fly data compilation, analysis and visualisation.

From OXALID to GlobaLID: Introducing a modern and FAIR lead isotope database with an interactive application

AbstractLead isotope provenance studies of archaeological artefacts rely crucially on the availability of reference data from raw material sources. The OXALID database, a collection of Excel sheets with Pb isotope data of ores and artefacts, is still the most cited data source in archaeometry. However, OXALID has not been updated for several years and contains almost exclusively data from Europe, particularly from the Mediterranean area. Digitalisation and open science philosophy currently revolutionise the use of machine‐generated data by developing digital data infrastructures. A modernised Pb isotope reference database, which is tailored for, but not limited to archaeometric research, is hence overdue. Here, we introduce GlobaLID, a FAIR (findable, accessible, interoperable, reusable) and extendable database and a web application with interactive and statistical tools for user‐friendly data handling up to publication quality. GlobaLID aims to be a collection point for worldwide Pb isotope data. It is designed as research infrastructure for Pb isotope studies in (for example) archaeometry, ore deposit and environmental geochemistry. As a community engagement project, GlobaLID invites scientists around the world to become active contributors to enable GlobaLID’s rapid growth. We released GlobaLID as a pilot study to showcase the infrastructure we build and provide a starting point for community discussion.

Tyto: A Python Tool Enabling Better Annotation Practices for Synthetic Biology Data-Sharing.

As synthetic biology becomes increasingly automated and data-driven, tools that help researchers implement FAIR (findable-accessible-interoperable-reusable) data management practices are needed. Crucially, in order to support machine processing and reusability of data, it is important that data artifacts are appropriately annotated with metadata drawn from controlled vocabularies. Unfortunately, adopting standardized annotation practices is difficult for many research groups to adopt, given the set of specialized database science skills usually required to interface with ontologies. In response to this need, Take Your Terms from Ontologies (Tyto) is a lightweight Python tool that supports the use of controlled vocabularies in everyday scripting practice. While Tyto has been developed for synthetic biology applications, its utility may extend to users working in other areas of bioinformatics research as well. Tyto is available as a Python package distribution or available as source at https://github.com/SynBioDex/tyto.

Guidelines for Publicly Archiving Terrestrial Model Data to Enhance Usability, Intercomparison, and Synthesis

Scientific communities are increasingly publishing data to evaluate, accredit, and build on published research. However, guidelines for curating data for publication are sparse for model-related research, limiting the usability of archived simulation data. In particular, there are no established guidelines for archiving data related to terrestrial models that simulate land processes and their coupled interactions with climate. Terrestrial modelers have a unique set of challenges when publishing data due to the diversity of scientific domains, research questions, and the types and scales of simulations. Researchers in the U.S. Department of Energy’s (DOE) projects use a variety of multiscale models to advance robust predictions of terrestrial and subsurface ecosystem processes. Here, we synthesize archiving needs for data associated with different DOE models, and provide guidelines for publishing terrestrial model data components following FAIR (Findable, Accessible, Interoperable, Reusable) principles. The guidelines recommend archiving model inputs and testing data used in final simulation runs along with associated codes, workflow scripts, and metadata in public repositories. Researchers should consider archiving model outputs if they are within the storage limits of the repository. We also provide considerations for how to bundle files into different data publications with citable digital object identifiers. Finally, we identify repository features and tools that would enable storage and reuse of model data. Given the diversity of DOE terrestrial models, these guidelines are transferable to other model types and will enable efficient reuse of simulation data for purposes such as model intercomparisons, initialization, benchmarking, synthesis, and comparisons with field observations.

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.

Community Data Mining Approach for Surface Complexation Database Development.

This paper presents a comprehensive data-to-model workflow, including a findable, accessible, interoperable, reusable (FAIR) community sorption database (newly developed LLNL Surface Complexation/Ion Exchange (L-SCIE) database) along with a data fitting workflow to efficiently optimize surface complexation reaction constants with multiple surface complexation model (SCM) constructs. This workflow serves as a universal framework to mine, compile, and analyze large numbers of published sorption data as well as to estimate reaction constants for parameterizing reactive transport models. The framework includes (1) data digitization from published papers, (2) data unification including unit conversions, and (3) data-model integration and reaction constant estimation using geochemical software PHREEQC coupled with the universal parameter estimation code PEST. We demonstrate our approach using an analysis of U(VI) sorption to quartz based on a first L-SCIE implementation, concluding that a multisite SCM construct with carbonate surface species yielded the best fit to community data. Surface complexation reaction constants extracted from this approach captured all available sorption data available in the literature and provided insight into previously published reaction constants and surface complexation model constructs. The L-SCIE sorption database presented herein allows for automating this approach across a wide range of metals and minerals and implementing novel machine learning approaches to reactive transport in the future.

Digital In Situ Data Collection in Earth Observation, Monitoring and Agriculture—Progress towards Digital Agriculture

Digital solutions in agricultural management promote food security and support the sustainable use of resources. As a result, remote sensing (RS) can be seen as an innovation for the fast generation of reliable information for agricultural management. Near real-time processed RS data can be used as a tool for decision making on multiple scales, from subplot to the global level. This high potential is not yet fully applied, due to often limited access to ground truth information, which is crucial for the development of transferable applications and acceptance. In this study we present a digital workflow for the acquisition, processing and dissemination of agroecological information based on proprietary and open-source software tools with state-of-the-art web-mapping technologies. Data is processed in near real-time and thus can be used as ground truth information to enhance quality and performance of RS-based products. Data is disseminated by easy-to-understand visualizations and download functionalities for specific application levels to serve specific user needs. It thus can increase expert knowledge and can be used for decision support at the same time. The fully digital workflow underpins the great potential to facilitate quality enhancement of future RS products in the context of precision agriculture by safeguarding data quality. The generated FAIR (findable, accessible, interoperable, reusable) datasets can be used to strengthen the relationship between scientists, initiatives and stakeholders.

The problem with open geospatial data for on‐farm research

AbstractScientists are under increased pressure to provide research data freely and openly to all interested parties as a means of furthering science. More than sharing data, there is an additional expectation that data comply to Findable, Accessible, Interoperable, Reusable (FAIR) principles. The requirement to share data presents challenges for farm geospatial data. The primary contention of this commentary is that data sharing requirements will make on‐farm research increasingly difficult while also not achieving the stated purposes of opening data. De‐identification of farm geospatial data is not sufficient to protect privacy, reducing likelihood of participation in research. Moreover, de‐identified farm geospatial data will have greatly reduced reusability. Limited guidance is available on appropriate mechanisms for sharing of farm geospatial data. This commentary briefly summarizes benefits and realities of data sharing, expands discussion to support the primary contention, and concludes with high‐level suggestions for moving forward.

Дослідження принципів, моделей та методів парадигми менеджменту наукових даних FAIR для аналізу метаданих BIG DATA

In this research work we considere the basic principles, models and methods of the FAIR (Findable, Accessible, Interoperable, Reusable) scientific data management paradigm as a separate case of Big Data. This paradigm is focused on the reuse of scientific research results.Basic principles of FAIR apply to three types of entities: data (or any digital object), metadata (information about this digital object) and infrastructure. Information on various projects, initiatives and communities working on solving the problems of scientific data and their metadata integration is examined. We analyze how the properties of FAIR data contribute to the unification and integration of the scientific infrastructure in the paradigm of open science, which is based on free access to research results and open data.