Data Stewardship Research Articles

Data Stewardship Wizard

Data Stewardship Wizard is a tool that facilitates the process of Data Management Planning / Data Stewardship Planning with a focus on the benefit to the research at hand.

Using Ontologies to Create Machine-Actionable Datasets: Two Case Studies

Achieving the highest levels of compliance with the FAIR (findable, accessible, interoperable, reusable) principles for scientific data management and stewardship requires machine-actionable semantic representations of data and metadata. Human and machine interpretation and reuse of measurement datasets rely on metrological information that is often specified inconsistently or cannot be inferred automatically, while several ontologies to capture the metrological information are available, practical implementation examples are few. This work aims to close this gap by discussing how standardised measurement data and metadata could be presented using semantic web technologies. The examples provided in this paper are machine-actionable descriptions of Earth observation and bathymetry measurement datasets, based on two ontologies of quantities and units of measurement selected for their prominence in the semantic web. The selected ontologies demonstrated a good coverage of the concepts related to quantities, dimensions, and individual units as well as systems of units, but showed variations and gaps in the coverage, completeness and traceability of other metrology concept representations such as standard uncertainty, expanded uncertainty, combined uncertainty, coverage factor, probability distribution, etc. These results highlight the need for both (I) user-friendly tools for semantic representations of measurement datasets and (II) the establishment of good practices within each scientific community. Further work will consequently investigate how to support ontology modelling for measurement uncertainty and associated concepts.

Foundations of machine learning for low-temperature plasmas: methods and case studies

Machine learning (ML) and artificial intelligence have proven to be an invaluable tool in tackling a vast array of scientific, engineering, and societal problems. The main drivers behind the recent proliferation of ML in practically all aspects of science and technology can be attributed to: (a) improved data acquisition and inexpensive data storage; (b) exponential growth in computing power; and (c) availability of open-source software and resources that have made the use of state-of-the-art ML algorithms widely accessible. The impact of ML on the field of low-temperature plasmas (LTPs) could be particularly significant in the emerging applications that involve plasma treatment of complex interfaces in areas ranging from the manufacture of microelectronics and processing of quantum materials, to the LTP-driven electrification of the chemical industry, and to medicine and biotechnology. This is primarily due to the complex and poorly-understood nature of the plasma-surface interactions in these applications that pose unique challenges to the modeling, diagnostics, and predictive control of LTPs. As the use of ML is becoming more prevalent, it is increasingly paramount for the LTP community to be able to critically analyze and assess the concepts and techniques behind data-driven approaches. To this end, the goal of this paper is to provide a tutorial overview of some of the widely-used ML methods that can be useful, amongst others, for discovering and correlating patterns in the data that may be otherwise impractical to decipher by human intuition alone, for learning multivariable nonlinear data-driven prediction models that are capable of describing the complex behavior of plasma interacting with interfaces, and for guiding the design of experiments to explore the parameter space of plasma-assisted processes in a systematic and resource-efficient manner. We illustrate the utility of various supervised, unsupervised and active learning methods using LTP datasets consisting of commonly-available, information-rich measurements (e.g. optical emission spectra, current–voltage characteristics, scanning electron microscope images, infrared surface temperature measurements, Fourier transform infrared spectra). All the ML demonstrations presented in this paper are carried out using open-source software; the datasets and codes are made publicly available. The FAIR guiding principles for scientific data management and stewardship can accelerate the adoption and development of ML in the LTP community.

Will It Ever Be FAIR?

AbstractA fundamental task of archaeology is to address challenging scientific questions related to the complexity of human societies. If we are to systematically understand the processes that affect human societies on multiple spatial and temporal scales, research leveraging existing archaeological data is essential. However, only a fraction of the data from archaeological projects are publicly findable or accessible, let alone interoperable or reusable. This is the case despite statements of disciplinary ethics, availability of capable technologies for data stewardship, publications providing guidance, and legal mandates. This article introduces the FAIR principles for data stewardship in North American archaeology, which state that data should be Findable, Accessible, Interoperable, and Reusable. We call for efforts to promote widespread adoption of the FAIR and CARE (Collective benefit, Authority to control, Responsibility, and Ethics) principles among professional organizations, publishers, data repositories, and researchers. We also call for adoption and implementation of requirements to adhere to these principles by governmental agencies, funding bodies, and other regulators of archaeological research. Ultimately, adoption of the FAIR principles in an ethical framework contributes to our understanding of our human experience and can lead to greater integration and reuse of research results, fostering increased partnerships between academia and industry.

FIP2DMP: Linking data management plans with FAIR implementation profiles

FIP2DMP is a mapping resource between a FAIR Implementation Profile (FIP) and a Data Management Plan (DMP) template implemented in the Data Stewardship Wizard. The main benefit of this resource is to facilitate easier adoption of community choices from the FIP by a researcher in their DMP.

MedicaidJS: a FAIR approach to real-time drug analytics

Abstract Motivation As prescription drug prices have drastically risen over the past decade, so has the need for real-time drug tracking resources. In spite of increased public availability to raw data sources, individual drug metrics remain concealed behind intricate nomenclature and complex data models. Some web applications, such as GoodRX, provide insight into real-time drug prices but offer limited interoperability. To overcome both obstacles we pursued the direct programmatic operation of the stateless Application Programming interfaces (HTTP REST APIs) maintained by the Food and Drug Administration (FDA), Medicaid, and National Library of Medicine. These data-intensive resources represent an opportunity to develop Software Development Kits (SDK) to streamline drug metrics without downloads or installations, in a manner that addresses the FAIR principles for stewardship in scientific data—Findability, Accessibility, Interoperability, and Reusability. These principles provide a guideline for continual stewardship of scientific data. Results MedicaidJS SDK was developed to orchestrate API calls to three complementary data resources: Medicaid (data.medicaid.gov), Food and Drug Administration (open.fda.gov), and the National Library of Medicine RxNorm (lhncbc.nlm.nih.gov/RxNav). MedicaidJS synthesizes response data from each platform into a zero-footprint JavaScript modular library that provides data wrangling, analysis, and generation of embeddable interactive visualizations. The SDK is served on github with live examples on observableHQ notebooks. It is freely available and can be embedded into web applications as modules returning structured JSON data with standardized identifiers. Availability and implementation Open source code publicly available at https://github.com/episphere/medicaid, live at episphere.github.io/medicaid, supplementary interactive Observable Notebooks at observablehq.com/@medicaidsdk/medicaidsdk.

Data Quality Management Strategy To Improve Remote Sensing Data Quality: A Case Study On National Remote Sensing Data Bank

National Remote Sensing Data Bank (Bank Data Penginderaan Jauh Nasional; BDPJN) is the operational implementer in the field of remote sensing to meet the needs of national data on remote sensing images. Remote sensing images are essential in the Indonesian government for various needs, such as in regional (spatial planning, city boundaries), disaster (forest fires, floods, landslides, earthquakes, volcanic eruptions), plantation, natural resources, and environment sectors. Quality management of BDPJN’s satellite images becomes challenging due to the increasing number of products owned and users annually. For this reason, a data quality management strategy is needed to guarantee and improve the quality of BDPJN data. To develop such a strategy, an assessment of the maturity of BDPJN’s data quality man- agement was conducted from the aspect of data processing by implementing Loshin’s Data Quality Management Maturity Model (DQM3) to find out the characteristics that were lacking. The results were then mapped based on Data Quality Management (DQM) activities in DAMA-DMBOK as a recommendation for data quality management strategies. This study applies quantitative research where data collection was done by distributing questionnaires to 24 respondents who are data stewards of medium, high, and very high-resolution mosaic images. Based on the assessment, BDPJN is in the maturity level of Defined to Managed. The recommendations are 21 DQM activities that can be carried out to improve BDPJN data quality.

Data Stewardship Plan templates designed to support the FAIR principles

Data Stewardship Plan (DSP) templates prompt users to consider various issues but typically have no requirements for actual implementation choices. But as FAIR methodologies mature the DSP will become a more directive “how to” manual for making data FAIR.

Data Stewards in Service of Artificial Intelligence: Reimagining Ai Futures Towards a Participatory Paradigm for Technological Innovation

Data Stewards in Service of Artificial Intelligence: Reimagining Ai Futures Towards a Participatory Paradigm for Technological Innovation

The N3C governance ecosystem: A model socio-technical partnership for the future of collaborative analytics at scale.

The National COVID Cohort Collaborative (N3C) is a public-private-government partnership established during the Coronavirus pandemic to create a centralized data resource called the "N3C data enclave." This resource contains individual-level health data from participating healthcare sites nationwide to support rapid collaborative analytics. N3C has enabled analytics within a cloud-based enclave of data from electronic health records from over 17 million people (with and without COVID-19) in the USA. To achieve this goal of a shared data resource, N3C implemented a shared governance strategy involving stakeholders in decision-making. The approach leveraged best practices in data stewardship and team science to rapidly enable COVID-19-related research at scale while respecting the privacy of data subjects and participating institutions. N3C balanced equitable access to data, team-based scientific productivity, and individual professional recognition - a key incentive for academic researchers. This governance approach makes N3C research sustainable and effective beyond the initial days of the pandemic. N3C demonstrated that shared governance can overcome traditional barriers to data sharing without compromising data security and trust. The governance innovations described herein are a helpful framework for other privacy-preserving data infrastructure programs and provide a working model for effective team science beyond COVID-19.

Informing the Global Data Future: Benchmarking Data Governance Frameworks

Abstract Data has become a critical trans-national and cross-border resource. Yet, the lack of a well-defined approach to using it poses challenges to harnessing its value. This article explores the increasing importance of global data governance due to the rapid growth of data, and the need for responsible data practices. The purpose of this paper is to compare approaches and identify patterns in the emergent data governance ecosystem within sectors close to the international development field, ultimately presenting key takeaways and reflections on when and why a global data governance framework may be needed. Overall, the paper provides information about the conditions when a more holistic, coordinated transnational approach to data governance may be needed to responsibly manage the global flow of data. The report does this by (a) considering conditions specified by the literature that may be conducive to global data governance, and (b) analyzing and comparing existing frameworks, specifically investigating six key elements: purpose, principles, anchoring documents, data description and lifecycle, processes, and practices. The article closes with a series of final recommendations, which include adopting a broader concept of data stewardship to reconcile data protection and promotion, focusing on responsible reuse of data to unlock socioeconomic value, harmonizing meanings to operationalize principles, incorporating global human rights frameworks to provide common North Stars, unifying key definitions of data, adopting a data lifecycle approach, incorporating participatory processes and collective agency, investing in new professions with specific roles, improving accountability through oversight and compliance mechanisms, and translating recommendations into practical tools.

Recording the ethical provenance of data and automating data stewardship

Health organisations use numerous different mechanisms to collect biomedical data, to determine the applicable ethical, legal and institutional conditions of use, and to reutilise the data in accordance with the relevant rules. These methods and mechanisms differ from one organisation to another, and involve considerable specialised human labour, including record-keeping functions and decision-making committees. In reutilising data at scale, however, organisations struggle to meet demands for data interoperability and for rapid inter-organisational data exchange due to reliance on legacy paper-based records and on the human-initiated administration of accompanying permissions in data. The adoption of permissions-recording, and permissions-administration tools that can be implemented at scale across numerous organisations is imperative. Further, these must be implemented in a manner that does not compromise the nuanced and contextual adjudicative processes of research ethics committees, data access committees, and biomedical research organisations. The tools required to implement a streamlined system of biomedical data exchange have in great part been developed. Indeed, there remains but a small core of functions that must further be standardised and automated to enable the recording and administration of permissions in biomedical research data with minimal human effort. Recording ethical provenance in this manner would enable biomedical data exchange to be performed at scale, in full respect of the ethical, legal, and institutional rules applicable to different datasets. This despite foundational differences between the distinct legal and normative frameworks is applicable to distinct communities and organisations that share data between one another.

Ontology-driven analysis of marine metagenomics: what more can we learn from our data?

The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data. Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments. In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.

Community-driven governance of FAIRness assessment: an open issue, an open discussion

Although FAIR Research Data Principles are targeted at and implemented by different communities, research disciplines, and research stakeholders (data stewards, curators, etc.), there is no conclusive way to determine the level of FAIRness intended or required to make research artefacts (including, but not limited to, research data) Findable, Accessible, Interoperable, and Reusable. The FAIR Principles cover all types of digital objects, metadata, and infrastructures. However, they focus their narrative on data features that support their reusability. FAIR defines principles, not standards, and therefore they do not propose a mechanism to achieve the behaviours they describe in an attempt to be technology/implementation neutral. A range of FAIR assessment metrics and tools have been designed that measure FAIRness. Unfortunately, the same digital objects assessed by different tools often exhibit widely different outcomes because of these independent interpretations of FAIR. This results in confusion among the publishers, the funders, and the users of digital research objects. Moreover, in the absence of a standard and transparent definition of what constitutes FAIR behaviours, there is a temptation to define existing approaches as being FAIR-compliant rather than having FAIR define the expected behaviours. This whitepaper identifies three high-level stakeholder categories -FAIR decision and policymakers, FAIR custodians, and FAIR practitioners - and provides examples outlining specific stakeholders' (hypothetical but anticipated) needs. It also examines possible models for governance based on the existing peer efforts, standardisation bodies, and other ways to acknowledge specifications and potential benefits. This whitepaper can serve as a starting point to foster an open discussion around FAIRness governance and the mechanism(s) that could be used to implement it, to be trusted, broadly representative, appropriately scoped, and sustainable. We invite engagement in this conversation in an open Google Group fair-assessment-governance@googlegroups.com

Towards FAIRification of sensitive and fragmented rare disease patient data: challenges and solutions in European reference network registries

IntroductionRare disease patient data are typically sensitive, present in multiple registries controlled by different custodians, and non-interoperable. Making these data Findable, Accessible, Interoperable, and Reusable (FAIR) for humans and machines at source enables federated discovery and analysis across data custodians. This facilitates accurate diagnosis, optimal clinical management, and personalised treatments. In Europe, twenty-four European Reference Networks (ERNs) work on rare disease registries in different clinical domains. The process and the implementation choices for making data FAIR (‘FAIRification’) differ among ERN registries. For example, registries use different software systems and are subject to different legal regulations. To support the ERNs in making informed decisions and to harmonise FAIRification, the FAIRification steward team was established to work as liaisons between ERNs and researchers from the European Joint Programme on Rare Diseases.ResultsThe FAIRification steward team inventoried the FAIRification challenges of the ERN registries and proposed solutions collectively with involved stakeholders to address them. Ninety-eight FAIRification challenges from 24 ERNs’ registries were collected and categorised into “training” (31), “community” (9), “modelling” (12), “implementation” (26), and “legal” (20). After curating and aggregating highly similar challenges, 41 unique FAIRification challenges remained. The two categories with the most challenges were “training” (15) and “implementation” (9), followed by “community” (7), and then “modelling” (5) and “legal” (5). To address all challenges, eleven types of solutions were proposed. Among them, the provision of guidelines and the organisation of training activities resolved the “training” challenges, which ranged from less-technical “coffee-rounds” to technical workshops, from informal FAIR Games to formal hackathons. Obtaining implementation support from technical experts was the solution type for tackling the “implementation” challenges.ConclusionThis work shows that a dedicated team of FAIR data stewards is an asset for harmonising the various processes of making data FAIR in a large organisation with multiple stakeholders. Additionally, multi-levelled training activities are required to accommodate the diverse needs of the ERNs. Finally, the lessons learned from the experience of the FAIRification steward team described in this paper may help to increase FAIR awareness and provide insights into FAIRification challenges and solutions of rare disease registries.

Data stewards in service of Artificial Intelligence: Reimagining AI futures towards a participatory paradigm for technological innovation

Data stewards in service of Artificial Intelligence: Reimagining AI futures towards a participatory paradigm for technological innovation

Legal Perspectives on Smart City Data as a Commons

Summary Smart cities are purported to produce vast amounts of data of immense value, both commercially and from a governance perspective. The control and stewardship of this smart city data remains controversial, with concerns for the role of the individual smart citizens and the control they exercise over the data they generate. Elinor Ostrom’s Nobel prize winning work on long-lasting and sustainable commons has been suggested as a solution, whereby the commons management principles would be applied to smart city data. This paper seeks to identify the current applications of Ostrom’s commons to smart city data in literature, as well as explore their legal implications. Particularly, what legal challenges may arise from the smart city data commons, and how they could be addressed through legislative frameworks. The article aims to identify and highlight these legal challenges and thereby provide a legal perspective on the concept of smart city data commons.

“Extremely slow and capricious”: A qualitative exploration of genetic researcher priorities in selecting shared data resources

PurposeGenetic researchers’ selection of a database can have scientific, regulatory, and ethical implications. It is important to understand what is driving database selection such that database stewards can be responsive to user needs while balancing the interests of communities in equitably benefiting from advances. MethodsWe conducted 23 semistructured interviews with US academic genetic researchers working with private, government, and collaboratory data stewards to explore factors that they consider when selecting a genetic database. ResultsInterviewees used existing databases to avoid burdens of primary data collection, which was described as expensive and time-consuming. They highlighted ease of access as the most important selection factor, integrating concepts of familiarity and efficiency. Data features, such as size and available phenotype, were also important. Demographic diversity was not originally cited by any interviewee as a pivotal factor; when probed, most stated that the option to consider diversity in database selection was limited. Database features, including integrity, harmonization, and storage were also described as key components of efficient use. ConclusionThere is a growing market and competition between genetic data stewards. Data need to be accessible, harmonized, and administratively supported for their existence to be translated into use and, in turn, result in scientific advancements across diverse communities.

Modeling community standards for metadata as templates makes data FAIR

It is challenging to determine whether datasets are findable, accessible, interoperable, and reusable (FAIR) because the FAIR Guiding Principles refer to highly idiosyncratic criteria regarding the metadata used to annotate datasets. Specifically, the FAIR principles require metadata to be “rich” and to adhere to “domain-relevant” community standards. Scientific communities should be able to define their own machine-actionable templates for metadata that encode these “rich,” discipline-specific elements. We have explored this template-based approach in the context of two software systems. One system is the CEDAR Workbench, which investigators use to author new metadata. The other is the FAIRware Workbench, which evaluates the metadata of archived datasets for their adherence to community standards. Benefits accrue when templates for metadata become central elements in an ecosystem of tools to manage online datasets—both because the templates serve as a community reference for what constitutes FAIR data, and because they embody that perspective in a form that can be distributed among a variety of software applications to assist with data stewardship and data sharing.

FAIR principles for AI models with a practical application for accelerated high energy diffraction microscopy

A concise and measurable set of FAIR (Findable, Accessible, Interoperable and Reusable) principles for scientific data is transforming the state-of-practice for data management and stewardship, supporting and enabling discovery and innovation. Learning from this initiative, and acknowledging the impact of artificial intelligence (AI) in the practice of science and engineering, we introduce a set of practical, concise, and measurable FAIR principles for AI models. We showcase how to create and share FAIR data and AI models within a unified computational framework combining the following elements: the Advanced Photon Source at Argonne National Laboratory, the Materials Data Facility, the Data and Learning Hub for Science, and funcX, and the Argonne Leadership Computing Facility (ALCF), in particular the ThetaGPU supercomputer and the SambaNova DataScale® system at the ALCF AI Testbed. We describe how this domain-agnostic computational framework may be harnessed to enable autonomous AI-driven discovery.