Metadata Framework Research Articles

Make data flow: Understanding the (re)usability of research data

Opening data and making datasets reusable is an extremely important and urgent need, especially as we move towards more data-driven studies worldwide. Various stakeholders are involved in the life cycle of data (re)use, including data providers/sharers, data (re)users, data managers/curators, and funding agencies. In response to the divergent demands of these stakeholders, data repositories have been established to bridge their needs and facilitate the cycle of data sharing and (re)use. However, recent studies have shown that data is being shared and (re)used through open data repositories at much lower levels than expected. This underscores a fundamental and often overlooked challenge in research data management, inviting a deeper and more comparative examination of the perspectives of various stakeholders on data (re)use. Using a mixed-method approach that includes metadata analysis, interview-based qualitative studies, and quantitative bibliometric analysis, this project first delves into the facilitating and inhibiting factors affecting a dataset's potential for (re)use, considering the perspectives of both data (re)users and data curators. It will then identify and elucidate the disparities between data (re)users and data curators, proposing suggestions for future data curation efforts. The findings will prompt data curators and data repositories to re-examine their current metadata frameworks and data curation practices, aligning them more closely with the actual needs of data (re)users. Moreover, this effort will make the flow of research data moves more smoothly within our academic communities, and contribute to the building of a more inclusive, equitable, open, and user-friendly research infrastructure.

Comparison of basal ganglia regions across murine brain atlases using metadata models and the Waxholm Space

The murine basal ganglia regions are targets for research into complex brain functions such as motor control and habit formation. However, there are several ways to name and annotate these regions, posing challenges for interpretation and comparison of data across studies. Here, we give an overview of basal ganglia terms and boundaries in the literature and reference atlases, and describe the criteria used for annotating these regions in the Waxholm Space rat brain atlas. We go on to compare basal ganglia annotations in stereotaxic rat brain atlases and the Allen Mouse brain Common Coordinate Framework to those in the Waxholm Space rat brain atlas. We demonstrate and describe considerable differences in the terms and boundaries of most basal ganglia regions across atlases and their versions. We also register information about atlases and regions in the openMINDS metadata framework, facilitating integration of data in neuroscience databases. The comparisons of terms and boundaries across rat and mouse atlases support analysis and interpretation of existing and new data from the basal ganglia.

Common Metadata Framework: Integrated Framework for Trustworthy Artificial Intelligence Pipelines

Common Metadata Framework: Integrated Framework for Trustworthy Artificial Intelligence Pipelines

《数据论文出版元数据》国家标准研制与实践

In August 2023, the national standard for GB/T 42813-2023 Data paper publication metadata was officially released. This standard specifies the content and framework of metadata required for data paper publication, including dataset metadata, data paper metadata, as well as their description methods, extension principles, and methods. It is applicable to the description, preservation, online publishing, and sharing services associated with data papers and their corresponding datasets. The release of this standard marks the first comprehensive agreement at the national level regarding the new mode of data paper publishing, namely the open sharing of scientific data, which has addressed the prior absence of standardized guidance in the field of data publishing. It facilitates data publishing institutions in promptly releasing data papers and their associated data, providing support for the rights and protection of scientific data. The standard holds significant importance in promoting the establishment of an open and shared ecosystem for scientific data. Since its publication, certain data journals or scientific data publishing platforms have begun adopting the elements and definitions specified in the standard, thus engaging in a more extensive practice.

Common Metadata Framework for Research Data Repository: Necessity to Support Open Science

Metadata is vital for information storage and retrieval from a database or repository. In the case of Research Data Repositories (RDRs), metadata can be a potent tool for describing and identifying data. Further, producing the metadata is indispensable for fostering data reuse. A filtered view of the registry of research data repositories, re3data.org, depicts no uniform patterns or standards for metadata in the case of RDRs, and the metadata elements and practices differ from RDR to RDR. The present study describes the features of a select number of RDRs and analyzes their metadata practices: Harvard Dataverse, Dryad, Figshare, Zenodo, and the Open Science Framework (OSF). It further examines the total number of metadata elements, common metadata elements, required metadata elements, and item-level metadata. Results indicate that even though Harvard Dataverse has the most metadata elements, Dryad provides rich metadata concerning item level. This study suggests a common metadata framework, richer metadata elements, and more features to make the research data’s interoperability possible from one RDR to another.

Building Flexible, Scalable, and Machine Learning-Ready Multimodal Oncology Datasets.

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS)-a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS consolidates over 41,000 cases from across repositories while achieving a high compression ratio relative to the 3.78 PB source data size. It offers sub-5-s query response times for interactive exploration. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

Museum Education Using XR Technologies: A Survey of Metadata Models

Museum education is a constantly evolving field that adapts to the changing needs and expectations of learners. By combining the unique assets of museums with innovative educational practices, the field continues to create enriching and engaging learning experiences. eXtended Reality technologies play a key role in this evolution, allowing museums to extend their reach and create more immersive, inclusive, and accessible educational experiences for a broader audience beyond their physical walls. Embracing well-structured and standardised metadata modelling is vital in achieving this vision. It can serve as the foundation that enables widespread interoperability and seamless integration of systems as well as in fostering synergies among the domains of cultural institutions, education, and XR technologies. This work surveys the historical and current state-of-the-art advancements in metadata models for each pillar of the work’s theme, namely the domains of education, cultural institutions, and XR while also detailing the key steps of metadata model amalgamation as a promising direction towards creating robust metadata frameworks from constituent models.

Ontologies for increasing the FAIRness of plant research data

The importance of improving the FAIRness (findability, accessibility, interoperability, reusability) of research data is undeniable, especially in the face of large, complex datasets currently being produced by omics technologies. Facilitating the integration of a dataset with other types of data increases the likelihood of reuse, and the potential of answering novel research questions. Ontologies are a useful tool for semantically tagging datasets as adding relevant metadata increases the understanding of how data was produced and increases its interoperability. Ontologies provide concepts for a particular domain as well as the relationships between concepts. By tagging data with ontology terms, data becomes both human- and machine- interpretable, allowing for increased reuse and interoperability. However, the task of identifying ontologies relevant to a particular research domain or technology is challenging, especially within the diverse realm of fundamental plant research. In this review, we outline the ontologies most relevant to the fundamental plant sciences and how they can be used to annotate data related to plant-specific experiments within metadata frameworks, such as Investigation-Study-Assay (ISA). We also outline repositories and platforms most useful for identifying applicable ontologies or finding ontology terms.

Semantics-Aware Document Retrieval for Government Administrative Data

The process of data analytics on large-scale government administrative data — that belong to various domains like education, transport, energy, and health — can be enhanced by retrieving pertinent documents from diverse data sources. Without a supporting framework of metadata, big data analytics can be daunting. Even though statistical algorithms can perform extensive analyses on a variety of data with little help from metadata, applying these techniques to heterogeneous data may not always result in reliable findings. Recently, semantics-aware (or semantic search) search techniques received much attention as they utilize implicit knowledge to enhance the search. Similarly, traditional search engines rely on the inherent linkages within the underlying data model to improve their search quality. In the case of general-purpose information retrieval systems, to gather information from the internet (open access data) or to access open government administrative data, a domain agnostic ontology shall be employed to supply background knowledge. This paper draws on research undertaken by the authors at IIIT Bangalore Center for Open Data Research (CODR) in developing a semantics-aware data lake framework to host and analyze government administrative data. In this study, we present an ontology-based document retrieval solution where an ontology serves as an intermediary to close the gap between what the user seeks and what the search retrieves. Although our study settings are based on the Government of Karnataka (GoK, India), we believe the findings have wider resonance. Our experimental results based on agricultural data from the GoK look promising.

A metadata framework for computational phenotypes.

With the burgeoning development of computational phenotypes, it is increasingly difficult to identify the right phenotype for the right tasks. This study uses a mixed-methods approach to develop and evaluate a novel metadata framework for retrieval of and reusing computational phenotypes. Twenty active phenotyping researchers from 2 large research networks, Electronic Medical Records and Genomics and Observational Health Data Sciences and Informatics, were recruited to suggest metadata elements. Once consensus was reached on 39 metadata elements, 47 new researchers were surveyed to evaluate the utility of the metadata framework. The survey consisted of 5-Likert multiple-choice questions and open-ended questions. Two more researchers were asked to use the metadata framework to annotate 8 type-2 diabetes mellitus phenotypes. More than 90% of the survey respondents rated metadata elements regarding phenotype definition and validation methods and metrics positively with a score of 4 or 5. Both researchers completed annotation of each phenotype within 60 min. Our thematic analysis of the narrative feedback indicates that the metadata framework was effective in capturing rich and explicit descriptions and enabling the search for phenotypes, compliance with data standards, and comprehensive validation metrics. Current limitations were its complexity for data collection and the entailed human costs.

FAIR data station for lightweight metadata management and validation of omics studies.

The life sciences are one of the biggest suppliers of scientific data. Reusing and connecting these data can uncover hidden insights and lead to new concepts. Efficient reuse of these datasets is strongly promoted when they are interlinked with a sufficient amount of machine-actionable metadata. While the FAIR (Findable, Accessible, Interoperable, Reusable) guiding principles have been accepted by all stakeholders, in practice, there are only a limited number of easy-to-adopt implementations available that fulfill the needs of data producers. We developed the FAIR Data Station, a lightweight application written in Java, that aims to support researchers in managing research metadata according to the FAIR principles. It implements the ISA metadata framework and uses minimal information metadata standards to capture experiment metadata. The FAIR Data Station consists of 3 modules. Based on the minimal information model(s) selected by the user, the "form generation module" creates a metadata template Excel workbook with a header row of machine-actionable attribute names. The Excel workbook is subsequently used by the data producer(s) as a familiar environment for sample metadata registration. At any point during this process, the format of the recorded values can be checked using the "validation module." Finally, the "resource module" can be used to convert the set of metadata recorded in the Excel workbook in RDF format, enabling (cross-project) (meta)data searches and, for publishing of sequence data, in an European Nucleotide Archive-compatible XML metadata file. Turning FAIR into reality requires the availability of easy-to-adopt data FAIRification workflows that are also of direct use for data producers. As such, the FAIR Data Station provides, in addition to the means to correctly FAIRify (omics) data, the means to build searchable metadata databases of similar projects and can assist in ENA metadata submission of sequence data. The FAIR Data Station is available at https://fairbydesign.nl.

A Multi-omics Data Analysis Workflow Packaged as a FAIR Digital Object

In current biomedical and complex trait research, increasing numbers of large molecular profiling (omics) data sets are being generated. At the same time, many studies fail to be reproduced (Baker 2016, Kim 2018). In order to improve study reproducibility and data reuse, including integration of data sets of different types and origins, it is imperative to work with omics data that is findable, accessible, interoperable, and reusable (FAIR, Wilkinson 2016) at the source. The data analysis, integration and stewardship pillar of the Netherlands X-omics Initiative aims to facilitate multi-omics research by providing tools to create, analyze and integrate FAIR omics data. We here report a joint activity of X-omics and the Netherlands Twin Register demonstrating the FAIRification of a multi-omics data set and the development of a FAIR multi-omics data analysis workflow. The implementation of FAIR principles (Wilkinson 2016) can improve scientific transparency and facilitate data reuse. However, Kim (2018) showed in a case study that the availability of data and code are required but not sufficient to reproduce data analyses. They highlighted the importance of interoperable and open formats, and structured metadata. In order to increase research reproducibility on the data analysis level, additional practices such as version-control, code licensing, and documentation have been proposed. These include recommendations for FAIR software by the Netherlands eScience Center and the Dutch Data Archiving and Networked Services (DANS), and FAIR principles for research software proposed by the Research Data Alliance (Chue Hong 2022). Data analysis in biomedical research usually comprises multiple steps often resulting in complex data analysis workflows and requiring additional practices, such as containerization, to ensure transparency and reproducibility (Goble 2020, Stoudt 2021). We apply these practices to a multi-omics data set that comprises genome-wide DNA methylation profiles, targeted metabolomics, and behavioral data of two cohorts that participated in the ACTION Biomarker Study (ACTION, Aggression in Children: Unraveling gene-environment interplay to inform Treatment and InterventiON strategies, see consortium members in Suppl. material 1) (Boomsma 2015, Bartels 2018, Hagenbeek 2020, van Dongen 2021, Hagenbeek 2022). The ACTION-NTR cohort consists of twins that are either longitudinally concordant or discordant for childhood aggression. The ACTION-Curium-LUMC cohort consists of children referred to the Dutch LUMC Curium academic center for child and youth psychiatry. With the joint analysis of multi-omics data and behavioral data, we aim to identify substructures in the ACTION-NTR cohort and link them to aggressive behavior. First, the individuals are clustered using Similarity Network Fusion (SNF, Wang 2014), and latent feature dimensions are uncovered using different unsupervised methods including Multi-Omics Factor Analysis (MOFA) (Argelaguet 2018) and Multiple Correspondence Analysis (MCA, Lê 2008, Husson 2017). In a second step, we determine correlations between -omics and phenotype dimensions, and use them to explain the subgroups of individuals from the ACTION-NTR cohort. In order to validate the results, we project data of the ACTION-Curium-LUMC cohort onto the latent dimensions and determine if correlations between omics and phenotype data can be reproduced. Integration of data across cohorts and across data types, requires interoperability. We applied different practices to make the data FAIR, including conversion of files to community-standard formats, and capturing experimental metadata using the ISA (Investigation, Study, Assay) metadata framework (Johnson 2021) and ontology-based annotations. All data analysis steps including pre-processing of different omics data types were implemented in either R or Python and combined in a modular Nextflow (Di Tommaso 2017) workflow, where the environment for each step is provided as a Singularity (Kurtzer 2017) container. The analysis workflow is packaged in a Research Object Crate (RO-Crate) (Soiland-Reyes 2022). The RO-Crate is a FAIR digital object that contains the Nextflow workflow including ontology-based annotations of each analysis step. Since omics data is considered to be potentially personally identifiable, the packaged workflow contains a minimal synthetic data set resembling the original data structure. Finally, the code is made available on GitHub and the workflow is registered at Workflowhub (Goble 2021). Since our Nextflow workflow is set up in a modular manner, the individual analysis steps can be reused in other workflows. We demonstrate this replicability by applying different sub-workflows to data from two different cohorts.

The Database Construction of Intangible Cultural Heritage Based on Artificial Intelligence

At present, the protection of material cultural heritage is spread all over the world, but the protection of intangible cultural heritage is relatively backward. With the development of information technology, database technology provides a new retrieval method. Therefore, based on database technology, this paper constructs the database system of intangible cultural heritage, where MySQL is used as the system database, Struts 2 framework is selected in MVC to realize the separation of business logic and data display, and retrieval and query are realized through Lucene. In addition, the system takes Mongolian stringed instruments as the carrier, constructs the metadata framework, and forms the database structure. Moreover, the system is divided into six functional modules and the front and back functions of the system are managed. Finally, the system function test and performance test are carried out. The test results show that the system has good functionality, which is helpful to realize the effective protection of intangible cultural heritage.

Metadata Framework to Support Deployment of Digital Health Technologies in Clinical Trials in Parkinson's Disease.

Sensor data from digital health technologies (DHTs) used in clinical trials provides a valuable source of information, because of the possibility to combine datasets from different studies, to combine it with other data types, and to reuse it multiple times for various purposes. To date, there exist no standards for capturing or storing DHT biosensor data applicable across modalities and disease areas, and which can also capture the clinical trial and environment-specific aspects, so-called metadata. In this perspectives paper, we propose a metadata framework that divides the DHT metadata into metadata that is independent of the therapeutic area or clinical trial design (concept of interest and context of use), and metadata that is dependent on these factors. We demonstrate how this framework can be applied to data collected with different types of DHTs deployed in the WATCH-PD clinical study of Parkinson’s disease. This framework provides a means to pre-specify and therefore standardize aspects of the use of DHTs, promoting comparability of DHTs across future studies.

Semantic Association and Decision-Making for the Internet of Things Based on Partial Differential Fuzzy Unsupervised Models

This study presents an in-depth study and analysis of IoT semantic association and decision-making using a partial differential fuzzy unsupervised approach. It focuses on a semantic annotation framework for device metadata and a knowledge base construction method to further improve the interoperability of IoT domain knowledge by building a unified IoT domain knowledge base and designing and implementing a semantic IoT knowledge management and application generation system. The main proposal is an IoT generic domain ontology, which reuses the existing excellent ontologies of IoT as much as possible, extracts the commonly used concepts of the domain and combines them, and provides a unified semantic template for IoT applications. On the other hand, by applying the entity linking technique to the extension of the knowledge base and linking the structured metadata of devices to the corresponding entities of the background knowledge base, the domain knowledge base can be made to share the rich background knowledge. At the same time, the interoperability of heterogeneous IoT metadata between applications is enhanced by unifying data and concepts from different device applications to the same background knowledge base through entity alignment techniques. The semantic representation of events applicable to IoT application scenarios is investigated, and an IoT event ontology for representing abstract events and event relationships in IoT is designed; next, a domain ontology with IoT sensing and control event representation capability is constructed based on the IoT event ontology, in which the typical domain ontology (SSN) that can be used for IoT applications is followed by the ontology reuse principle is improved and extended to support the description of event types and interevent relationships, and the IoT event model is associated with the improved IoT base ontology through an ontology alignment approach. Finally, the IoT sensing and control ontology are validated by semantic modeling of device composition, component relationships, and operational processes based on the IoT sensing and control ontology.

Satu Data Indonesia in Sectoral Statistics: Concept of Satu Data Metadata Framework (SDMF)

Satu Data Indonesia is a policy contrive to encourage the problem of inadequate data governance in Indonesia. This policy makes 4 main principles, namely metadata, data standards, reference codes, and interoperability as metrics of success in its implementation. In this study, we analyze the satu data Indonesia implementation in Kutai Timur Regency. We found that the integration of the satu data principle is challenging to apply technically because sectoral data in Indonesia has 2 characteristics based on the preparation of the list of data needs, namely the centralized data list, and the decentralized data list. Decentralized data list is a list of data that is partially prepared in each agency without any coordination with other stakeholders for completing the satu data principles. To accommodating this condition, we design the Satu Data Metadata Framework (SDMF) a data standard framework that is in accordance with the conditions of data governance in Indonesia. SDMF utilizes contextual layer and discovery layer of metadata to provide temporal attribute called Satu Data Resource Identifier (SDRI) for integration purpose

Addressing the Challenges of Describing Alternative Format Materials: A Metadata Framework to Enhance Information Accessibility of People with Disabilities

Addressing the Challenges of Describing Alternative Format Materials: A Metadata Framework to Enhance Information Accessibility of People with Disabilities

A Metadata Framework for Asset Management Decision Support: A Water Infrastructure Case Study

A water utility requires myriads of data for effective decision-making. As the sources and ranges of data are becoming increasingly complex, the use of a metadata framework can play a significant role in effective data management. Using case study method, this research analyzed data needs of a water supply system in a small town in South Australia and designed a demo portal of a metadata framework. As part of the case study, the project team undertook a broad investigative approach using focus group (interviews), observation, exploration of potential data sources, identification of knowledge leaders and information technology systems. The metadata framework comprised two separate but interconnected metadata groups, (1) metadata elements to describe the metadata source and (2) metadata elements to describe the datasets held in each data source. The metadata framework was populated to describe data sources and data held in each of the sources. The data catalogue created by this process showed that it was accomplishable and appropriate to describe data sources and datasets via a metadata framework.

Approaches and Criteria for Provenance in Biomedical Data Sets and Workflows: Protocol for a Scoping Review

BackgroundProvenance supports the understanding of data genesis, and it is a key factor to ensure the trustworthiness of digital objects containing (sensitive) scientific data. Provenance information contributes to a better understanding of scientific results and fosters collaboration on existing data as well as data sharing. This encompasses defining comprehensive concepts and standards for transparency and traceability, reproducibility, validity, and quality assurance during clinical and scientific data workflows and research.ObjectiveThe aim of this scoping review is to investigate existing evidence regarding approaches and criteria for provenance tracking as well as disclosing current knowledge gaps in the biomedical domain. This review covers modeling aspects as well as metadata frameworks for meaningful and usable provenance information during creation, collection, and processing of (sensitive) scientific biomedical data. This review also covers the examination of quality aspects of provenance criteria.MethodsThis scoping review will follow the methodological framework by Arksey and O'Malley. Relevant publications will be obtained by querying PubMed and Web of Science. All papers in English language will be included, published between January 1, 2006 and March 23, 2021. Data retrieval will be accompanied by manual search for grey literature. Potential publications will then be exported into a reference management software, and duplicates will be removed. Afterwards, the obtained set of papers will be transferred into a systematic review management tool. All publications will be screened, extracted, and analyzed: title and abstract screening will be carried out by 4 independent reviewers. Majority vote is required for consent to eligibility of papers based on the defined inclusion and exclusion criteria. Full-text reading will be performed independently by 2 reviewers and in the last step, key information will be extracted on a pretested template. If agreement cannot be reached, the conflict will be resolved by a domain expert. Charted data will be analyzed by categorizing and summarizing the individual data items based on the research questions. Tabular or graphical overviews will be given, if applicable.ResultsThe reporting follows the extension of the Preferred Reporting Items for Systematic reviews and Meta-Analyses statements for Scoping Reviews. Electronic database searches in PubMed and Web of Science resulted in 469 matches after deduplication. As of September 2021, the scoping review is in the full-text screening stage. The data extraction using the pretested charting template will follow the full-text screening stage. We expect the scoping review report to be completed by February 2022.ConclusionsInformation about the origin of healthcare data has a major impact on the quality and the reusability of scientific results as well as follow-up activities. This protocol outlines plans for a scoping review that will provide information about current approaches, challenges, or knowledge gaps with provenance tracking in biomedical sciences.International Registered Report Identifier (IRRID)DERR1-10.2196/31750

ISA API: An open platform for interoperable life science experimental metadata.

BackgroundThe Investigation/Study/Assay (ISA) Metadata Framework is an established and widely used set of open source community specifications and software tools for enabling discovery, exchange, and publication of metadata from experiments in the life sciences. The original ISA software suite provided a set of user-facing Java tools for creating and manipulating the information structured in ISA-Tab—a now widely used tabular format. To make the ISA framework more accessible to machines and enable programmatic manipulation of experiment metadata, the JSON serialization ISA-JSON was developed.ResultsIn this work, we present the ISA API, a Python library for the creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats by using a common data model engineered as Python object classes. We describe the ISA API feature set, early adopters, and its growing user community.ConclusionsThe ISA API provides users with rich programmatic metadata-handling functionality to support automation, a common interface, and an interoperable medium between the 2 ISA formats, as well as with other life science data formats required for depositing data in public databases.