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Histochemistry and Cell Biology Sep 2023Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have...
Biological imaging is one of the primary tools by which we understand living systems across scales from atoms to organisms. Rapid advances in imaging technology have increased both the spatial and temporal resolutions at which we examine those systems, as well as enabling visualisation of larger tissue volumes. These advances have huge potential but also generate ever increasing amounts of imaging data that must be stored and analysed. Public image repositories provide a critical scientific service through open data provision, supporting reproducibility of scientific results, access to reference imaging datasets and reuse of data for new scientific discovery and acceleration of image analysis methods development. The scale and scope of imaging data provides both challenges and opportunities for open sharing of image data. In this article, we provide a perspective influenced by decades of provision of open data resources for biological information, suggesting areas to focus on and a path towards global interoperability.
Topics: Reproducibility of Results; Image Processing, Computer-Assisted
PubMed: 37537341
DOI: 10.1007/s00418-023-02216-2 -
Healthcare Informatics Research Jul 2023In the era of the Fourth Industrial Revolution, where an ecosystem is being developed to enhance the quality of healthcare services by applying information and...
OBJECTIVES
In the era of the Fourth Industrial Revolution, where an ecosystem is being developed to enhance the quality of healthcare services by applying information and communication technologies, systematic and sustainable data management is essential for medical institutions. In this study, we assessed the data management status and emerging concerns of three medical institutions, while also examining future directions for seamless data management.
METHODS
To evaluate the data management status, we examined data types, capacities, infrastructure, backup methods, and related organizations. We also discussed challenges, such as resource and infrastructure issues, problems related to government regulations, and considerations for future data management.
RESULTS
Hospitals are grappling with the increasing data storage space and a shortage of management personnel due to costs and project termination, which necessitates countermeasures and support. Data management regulations on the destruction or maintenance of medical records are needed, and institutional consideration for secondary utilization such as long-term treatment or research is required. Government-level guidelines for facilitating hospital data sharing and mobile patient services should be developed. Additionally, hospital executives at the organizational level need to make efforts to facilitate the clinical validation of artificial intelligence software.
CONCLUSIONS
This analysis of the current status and emerging issues of data management reveals potential solutions and sets the stage for future organizational and policy directions. If medical big data is systematically managed, accumulated over time, and strategically monetized, it has the potential to create new value.
PubMed: 37591676
DOI: 10.4258/hir.2023.29.3.209 -
Global Challenges (Hoboken, NJ) Jan 2024The explosive growth of biomedical Big Data presents both significant opportunities and challenges in the realm of knowledge discovery and translational applications... (Review)
Review
The explosive growth of biomedical Big Data presents both significant opportunities and challenges in the realm of knowledge discovery and translational applications within precision medicine. Efficient management, analysis, and interpretation of big data can pave the way for groundbreaking advancements in precision medicine. However, the unprecedented strides in the automated collection of large-scale molecular and clinical data have also introduced formidable challenges in terms of data analysis and interpretation, necessitating the development of novel computational approaches. Some potential challenges include the curse of dimensionality, data heterogeneity, missing data, class imbalance, and scalability issues. This overview article focuses on the recent progress and breakthroughs in the application of big data within precision medicine. Key aspects are summarized, including content, data sources, technologies, tools, challenges, and existing gaps. Nine fields-Datawarehouse and data management, electronic medical record, biomedical imaging informatics, Artificial intelligence-aided surgical design and surgery optimization, omics data, health monitoring data, knowledge graph, public health informatics, and security and privacy-are discussed.
PubMed: 38223896
DOI: 10.1002/gch2.202300163 -
A longitudinal resource for population neuroscience of school-age children and adolescents in China.Scientific Data Aug 2023During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era...
During the past decade, cognitive neuroscience has been calling for population diversity to address the challenge of validity and generalizability, ushering in a new era of population neuroscience. The developing Chinese Color Nest Project (devCCNP, 2013-2022), the first ten-year stage of the lifespan CCNP (2013-2032), is a two-stages project focusing on brain-mind development. The project aims to create and share a large-scale, longitudinal and multimodal dataset of typically developing children and adolescents (ages 6.0-17.9 at enrolment) in the Chinese population. The devCCNP houses not only phenotypes measured by demographic, biophysical, psychological and behavioural, cognitive, affective, and ocular-tracking assessments but also neurotypes measured with magnetic resonance imaging (MRI) of brain morphometry, resting-state function, naturalistic viewing function and diffusion structure. This Data Descriptor introduces the first data release of devCCNP including a total of 864 visits from 479 participants. Herein, we provided details of the experimental design, sampling strategies, and technical validation of the devCCNP resource. We demonstrate and discuss the potential of a multicohort longitudinal design to depict normative brain growth curves from the perspective of developmental population neuroscience. The devCCNP resource is shared as part of the "Chinese Data-sharing Warehouse for In-vivo Imaging Brain" in the Chinese Color Nest Project (CCNP) - Lifespan Brain-Mind Development Data Community ( https://ccnp.scidb.cn ) at the Science Data Bank.
Topics: Humans; Asian People; Brain; China; Data Warehousing; Databases, Factual; Neurosciences
PubMed: 37604823
DOI: 10.1038/s41597-023-02377-8 -
Health Research Policy and Systems Jul 2023Digital transformation in healthcare and the growth of health data generation and collection are important challenges for the secondary use of healthcare records in the...
BACKGROUND
Digital transformation in healthcare and the growth of health data generation and collection are important challenges for the secondary use of healthcare records in the health research field. Likewise, due to the ethical and legal constraints for using sensitive data, understanding how health data are managed by dedicated infrastructures called data hubs is essential to facilitating data sharing and reuse.
METHODS
To capture the different data governance behind health data hubs across Europe, a survey focused on analysing the feasibility of linking individual-level data between data collections and the generation of health data governance patterns was carried out. The target audience of this study was national, European, and global data hubs. In total, the designed survey was sent to a representative list of 99 health data hubs in January 2022.
RESULTS
In total, 41 survey responses received until June 2022 were analysed. Stratification methods were performed to cover the different levels of granularity identified in some data hubs' characteristics. Firstly, a general pattern of data governance for data hubs was defined. Afterward, specific profiles were defined, generating specific data governance patterns through the stratifications in terms of the kind of organization (centralized versus decentralized) and role (data controller or data processor) of the health data hub respondents.
CONCLUSIONS
The analysis of the responses from health data hub respondents across Europe provided a list of the most frequent aspects, which concluded with a set of specific best practices on data management and governance, taking into account the constraints of sensitive data. In summary, a data hub should work in a centralized way, providing a Data Processing Agreement and a formal procedure to identify data providers, as well as data quality control, data integrity and anonymization methods.
Topics: Humans; Data Accuracy; Data Collection; Data Management; Europe; Health Facilities
PubMed: 37430347
DOI: 10.1186/s12961-023-01026-1 -
Frontiers in Neurology 2023Efficient data sharing is hampered by an array of organizational, ethical, behavioral, and technical challenges, slowing research progress and reducing the utility of... (Review)
Review
Efficient data sharing is hampered by an array of organizational, ethical, behavioral, and technical challenges, slowing research progress and reducing the utility of data generated by clinical research studies on neurodegenerative diseases. There is a particular need to address differences between public and private sector environments for research and data sharing, which have varying standards, expectations, motivations, and interests. The Neuronet data sharing Working Group was set up to understand the existing barriers to data sharing in public-private partnership projects, and to provide guidance to overcome these barriers, by convening data sharing experts from diverse projects in the IMI neurodegeneration portfolio. In this policy and practice review, we outline the challenges and learnings of the WG, providing the neurodegeneration community with examples of good practices and recommendations on how to overcome obstacles to data sharing. These obstacles span organizational issues linked to the unique structure of cross-sectoral, collaborative research initiatives, to technical issues that affect the storage, structure and annotations of individual datasets. We also identify sociotechnical hurdles, such as academic recognition and reward systems that disincentivise data sharing, and legal challenges linked to heightened perceptions of data privacy risk, compounded by a lack of clear guidance on GDPR compliance mechanisms for public-private research. Focusing on real-world, neuroimaging and digital biomarker data, we highlight particular challenges and learnings for data sharing, such as data management planning, development of ethical codes of conduct, and harmonization of protocols and curation processes. Cross-cutting solutions and enablers include the principles of transparency, standardization and co-design - from open, accessible metadata catalogs that enhance findability of data, to measures that increase visibility and trust in data reuse.
PubMed: 37545729
DOI: 10.3389/fneur.2023.1187095 -
Frontiers in Bioinformatics 2023As biological imaging continues to rapidly advance, it results in increasingly complex image data, necessitating a reevaluation of conventional bioimage analysis methods...
As biological imaging continues to rapidly advance, it results in increasingly complex image data, necessitating a reevaluation of conventional bioimage analysis methods and their accessibility. This perspective underscores our belief that a transition from desktop-based tools to web-based bioimage analysis could unlock immense opportunities for improved accessibility, enhanced collaboration, and streamlined workflows. We outline the potential benefits, such as reduced local computational demands and solutions to common challenges, including software installation issues and limited reproducibility. Furthermore, we explore the present state of web-based tools, hurdles in implementation, and the significance of collective involvement from the scientific community in driving this transition. In acknowledging the potential roadblocks and complexity of data management, we suggest a combined approach of selective prototyping and large-scale workflow application for optimal usage. Embracing web-based bioimage analysis could pave the way for the life sciences community to accelerate biological research, offering a robust platform for a more collaborative, efficient, and democratized science.
PubMed: 37560357
DOI: 10.3389/fbinf.2023.1233748 -
Patient Safety in Surgery Jun 2024Digital data processing has revolutionized medical documentation and enabled the aggregation of patient data across hospitals. Initiatives such as those from the AO... (Review)
Review
Digital data processing has revolutionized medical documentation and enabled the aggregation of patient data across hospitals. Initiatives such as those from the AO Foundation about fracture treatment (AO Sammelstudie, 1986), the Major Trauma Outcome Study (MTOS) about survival, and the Trauma Audit and Research Network (TARN) pioneered multi-hospital data collection. Large trauma registries, like the German Trauma Registry (TR-DGU) helped improve evidence levels but were still constrained by predefined data sets and limited physiological parameters. The improvement in the understanding of pathophysiological reactions substantiated that decision making about fracture care led to development of patient's tailored dynamic approaches like the Safe Definitive Surgery algorithm. In the future, artificial intelligence (AI) may provide further steps by potentially transforming fracture recognition and/or outcome prediction. The evolution towards flexible decision making and AI-driven innovations may be of further help. The current manuscript summarizes the development of big data from local databases and subsequent trauma registries to AI-based algorithms, such as Parkland Trauma Mortality Index and the IBM Watson Pathway Explorer.
PubMed: 38902828
DOI: 10.1186/s13037-024-00404-0 -
JCO Clinical Cancer Informatics Sep 2023Osteosarcoma research advancement requires enhanced data integration across different modalities and sources. Current osteosarcoma research, encompassing clinical,...
PURPOSE
Osteosarcoma research advancement requires enhanced data integration across different modalities and sources. Current osteosarcoma research, encompassing clinical, genomic, protein, and tissue imaging data, is hindered by the siloed landscape of data generation and storage.
MATERIALS AND METHODS
Clinical, molecular profiling, and tissue imaging data for 573 patients with pediatric osteosarcoma were collected from four public and institutional sources. A common data model incorporating standardized terminology was created to facilitate the transformation, integration, and load of source data into a relational database. On the basis of this database, a data commons accompanied by a user-friendly web portal was developed, enabling various data exploration and analytics functions.
RESULTS
The Osteosarcoma Explorer (OSE) was released to the public in 2021. Leveraging a comprehensive and harmonized data set on the backend, the OSE offers a wide range of functions, including Cohort Discovery, Patient Dashboard, Image Visualization, and Online Analysis. Since its initial release, the OSE has experienced an increasing utilization by the osteosarcoma research community and provided solid, continuous user support. To our knowledge, the OSE is the largest (N = 573) and most comprehensive research data commons for pediatric osteosarcoma, a rare disease. This project demonstrates an effective framework for data integration and data commons development that can be readily applied to other projects sharing similar goals.
CONCLUSION
The OSE offers an online exploration and analysis platform for integrated clinical, molecular profiling, and tissue imaging data of osteosarcoma. Its underlying data model, database, and web framework support continuous expansion onto new data modalities and sources.
Topics: Child; Humans; Databases, Factual; Data Management; Genomics; Osteosarcoma
PubMed: 37956387
DOI: 10.1200/CCI.23.00104 -
Blockchain in Healthcare Today 2024Properly managing healthcare data is a complex endeavor that must balance the requirements and interests of many stakeholders. In this paper, we present the findings... (Review)
Review
Properly managing healthcare data is a complex endeavor that must balance the requirements and interests of many stakeholders. In this paper, we present the findings from a panel discussion with healthcare professionals and academics, who elaborate on the current situation in healthcare data management as well as the future role that blockchain could play in this sector. Based on the findings of this panel, we structure the research field of healthcare data management and provide numerous avenues for future research. The outcome is a framework that highlights the important role of healthcare data and puts them into context. From a patient's perspective, we specifically elaborate on trust and privacy as well as the expected benefits. Additionally, four important data aspects are identified: integrity, security, interoperability, and, finally, sharing and transfer. We also outline the importance of current problems and derive several relevant and timely research questions that build the foundation of a research agenda for blockchain-driven innovation in healthcare data management. In summary, the framework will inform practitioners of blockchain's potential in healthcare and structure the area for researchers, who are called upon to investigate the respective topics in greater detail.
PubMed: 38715763
DOI: 10.30953/bhty.v7.301