Biomedical data management and processing - a new framework

The integration of information from biomedical devices is of fundamental importance for effective medical diagnosis. In this sense, the present work aimed to develop a new framework able to manage and process biomedical data in real time. The major advantage of the proposed solution is the ability to add new medical devices and integrate their results with the existing ones. The devices tested include brainwave sensors, a baropodometric treadmill and a biomedical kit composed of a patient position sensor (accelerometer), glucometer, body temperature, blood pressure, pulse and oxygen in blood, airflow, galvanic skin response and electrocardiogram sensors. From the tests conducted, it can be concluded that the proposed framework is robust, accurate and fast, and can manage and process large volumes of data in real time. Customizable graphs can be built from the electroencephalogramsignals acquired during patient gait, which can be analyzed based on barographic image registration. Finally, it can be concluded that the framework is quite promising to be used to assist medical diagnosis and improve and accelerate the treatment of patients

A Query Integrator and Manager for the Query Web

We introduce two concepts: the Query Web as a layer of interconnected queries over the document web and the semantic web, and a Query Web Integrator and Manager (QI) that enables the Query Web to evolve. QI permits users to write, save and reuse queries over any web accessible source, including other queries saved in other installations of QI. The saved queries may be in any language (e.g. SPARQL, XQuery); the only condition for interconnection is that the queries return their results in some form of XML. This condition allows queries to chain off each other, and to be written in whatever language is appropriate for the task. We illustrate the potential use of QI for several biomedical use cases, including ontology view generation using a combination of graph-based and logical approaches, value set generation for clinical data management, image annotation using terminology obtained from an ontology web service, ontology-driven brain imaging data integration, small-scale clinical data integration, and wider-scale clinical data integration. Such use cases illustrate the current range of applications of QI and lead us to speculate about the potential evolution from smaller groups of interconnected queries into a larger query network that layers over the document and semantic web. The resulting Query Web could greatly aid researchers and others who now have to manually navigate through multiple information sources in order to answer specific questions

Data Publications Correlate with Citation Impact

Neuroscience and molecular biology have been generating large datasets over the past years that are reshaping how research is being conducted. In their wake, open data sharing has been singled out as a major challenge for the future of research. We conducted a comparative study of citations of data publications in both fields, showing that the average publication tagged with a data-related term by the NCBI MeSH (Medical Subject Headings) curators achieves a significantly larger citation impact than the average in either field. We introduce a new metric, the data article citation index (DAC-index), to identify the most prolific authors among those data-related publications. The study is fully reproducible from an executable Rmd (R Markdown) script together with all the citation datasets. We hope these results can encourage authors to more openly publish their data

MRI data quality assessment for the RIN - Neuroimaging Network using the ACR phantoms

PURPOSE: Generating big-data is becoming imperative with the advent of machine learning. RIN-Neuroimaging Network addresses this need by developing harmonized protocols for multisite studies to identify quantitative MRI (qMRI) biomarkers for neurological diseases. In this context, image quality control (QC) is essential. Here, we present methods and results of how the RIN performs intra- and inter-site reproducibility of geometrical and image contrast parameters, demonstrating the relevance of such QC practice. METHODS: American College of Radiology (ACR) large and small phantoms were selected. Eighteen sites were equipped with a 3T scanner that differed by vendor, hardware/software versions, and receiver coils. The standard ACR protocol was optimized (in-plane voxel, post-processing filters, receiver bandwidth) and repeated monthly. Uniformity, ghosting, geometric accuracy, ellipse’s ratio, slice thickness, and high-contrast detectability tests were performed using an automatic QC script. RESULTS: Measures were mostly within the ACR tolerance ranges for both T1- and T2-weighted acquisitions, for all scanners, regardless of vendor, coil, and signal transmission chain type. All measurements showed good reproducibility over time. Uniformity and slice thickness failed at some sites. Scanners that upgraded the signal transmission chain showed a decrease in geometric distortion along the slice encoding direction. Inter-vendor differences were observed in uniformity and geometric measurements along the slice encoding direction (i.e. ellipse’s ratio). CONCLUSIONS: Use of the ACR phantoms highlighted issues that triggered interventions to correct performance at some sites and to improve the longitudinal stability of the scanners. This is relevant for establishing precision levels for future multisite studies of qMRI biomarkers

FlywheelTools: Data Curation and Manipulation on the Flywheel Platform

The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data. Flywheel is one such database platform that offers easily accessible, large-scale data management, along with a framework for reproducible analyses through containerized pipelines. The Brain Imaging Data Structure (BIDS) is the de facto standard for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task. In particular, standard solutions for BIDS curation are limited on Flywheel. To address these challenges, we developed “FlywheelTools,” a software toolbox for reproducible data curation and manipulation on Flywheel. FlywheelTools includes two elements: fw-heudiconv, for heuristic-driven curation of data into BIDS, and flaudit, which audits and inventories projects on Flywheel. Together, these tools accelerate reproducible neuroscience research on the widely used Flywheel platform

Data sharing in neuroimaging research

Significant resources around the world have been invested in neuroimaging studies of brain function and disease. Easier access to this large body of work should have profound impact on research in cognitive neuroscience and psychiatry, leading to advances in the diagnosis and treatment of psychiatric and neurological disease. A trend toward increased sharing of neuroimaging data has emerged in recent years. Nevertheless, a number of barriers continue to impede momentum. Many researchers and institutions remain uncertain about how to share data or lack the tools and expertise to participate in data sharing. The use of electronic data capture (EDC) methods for neuroimaging greatly simplifies the task of data collection and has the potential to help standardize many aspects of data sharing. We review here the motivations for sharing neuroimaging data, the current data sharing landscape, and the sociological or technical barriers that still need to be addressed. The INCF Task Force on Neuroimaging Datasharing, in conjunction with several collaborative groups around the world, has started work on several tools to ease and eventually automate the practice of data sharing. It is hoped that such tools will allow researchers to easily share raw, processed, and derived neuroimaging data, with appropriate metadata and provenance records, and will improve the reproducibility of neuroimaging studies. By providing seamless integration of data sharing and analysis tools within a commodity research environment, the Task Force seeks to identify and minimize barriers to data sharing in the field of neuroimaging

Enabling collaborative research using the Biomedical Informatics Research Network (BIRN)

Objective As biomedical technology becomes increasingly sophisticated, researchers can probe ever more subtle effects with the added requirement that the investigation of small effects often requires the acquisition of large amounts of data. In biomedicine, these data are often acquired at, and later shared between, multiple sites. There are both technological and sociological hurdles to be overcome for data to be passed between researchers and later made accessible to the larger scientific community. The goal of the Biomedical Informatics Research Network (BIRN) is to address the challenges inherent in biomedical data sharing. Materials and methods BIRN tools are grouped into ‘capabilities’ and are available in the areas of data management, data security, information integration, and knowledge engineering. BIRN has a user-driven focus and employs a layered architectural approach that promotes reuse of infrastructure. BIRN tools are designed to be modular and therefore can work with pre-existing tools. BIRN users can choose the capabilities most useful for their application, while not having to ensure that their project conforms to a monolithic architecture. Results BIRN has implemented a new software-based data-sharing infrastructure that has been put to use in many different domains within biomedicine. BIRN is actively involved in outreach to the broader biomedical community to form working partnerships. Conclusion BIRN's mission is to provide capabilities and services related to data sharing to the biomedical research community. It does this by forming partnerships and solving specific, user-driven problems whose solutions are then available for use by other groups.National Center for Research Resources (U.S.) (U24-RR025736)National Center for Research Resources (U.S.) (U24-RR021992)National Center for Research Resources (U.S.) (U24-RR021760)National Center for Research Resources (U.S.) (U24-RR026057-01)National Institute of General Medical Sciences (U.S.) (NIGMS; RO1 GM083871)National Science Foundation (U.S.) (grant 0849977)Michael J. Fox Foundation for Parkinson's ResearchKinetics Foundatio

Dataremix: Aesthetic Experiences of Big Data and Data Abstraction

This PhD by published work expands on the contribution to knowledge in two recent large-scale transdisciplinary artistic research projects: ATLAS in silico and INSTRUMENT | One Antarctic Night and their exhibited and published outputs. The thesis reflects upon this practice-based artistic research that interrogates data abstraction: the digitization, datafication and abstraction of culture and nature, as vast and abstract digital data. The research is situated in digital arts practices that engage a combination of big (scientific) data as artistic material, embodied interaction in virtual environments, and poetic recombination. A transdisciplinary and collaborative artistic practice, x-resonance, provides a framework for the hybrid processes, outcomes, and contributions to knowledge from the research. These are purposefully and productively situated at the objective | subjective interface, have potential to convey multiple meanings simultaneously to a variety of audiences and resist disciplinary definition. In the course of the research, a novel methodology emerges, dataremix, which is employed and iteratively evolved through artistic practice to address the research questions: 1) How can a visceral and poetic experience of data abstraction be created? and 2) How would one go about generating an artistically-informed (scientific) discovery? Several interconnected contributions to knowledge arise through the first research question: creation of representational elements for artistic visualization of big (scientific) data that includes four new forms (genomic calligraphy, algorithmic objects as natural specimens, scalable auditory data signatures, and signal objects); an aesthetic of slowness that contributes an extension to the operative forces in Jevbratt’s inverted sublime of looking down and in to also include looking fast and slow; an extension of Corby’s objective and subjective image consisting of “informational and aesthetic components” to novel virtual environments created from big 3 (scientific) data that extend Davies’ poetic virtual spatiality to poetic objective | subjective generative virtual spaces; and an extension of Seaman’s embodied interactive recombinant poetics through embodied interaction in virtual environments as a recapitulation of scientific (objective) and algorithmic processes through aesthetic (subjective) physical gestures. These contributions holistically combine in the artworks ATLAS in silico and INSTRUMENT | One Antarctic Night to create visceral poetic experiences of big data abstraction. Contributions to knowledge from the first research question develop artworks that are visceral and poetic experiences of data abstraction, and which manifest the objective | subjective through art. Contributions to knowledge from the second research question occur through the process of the artworks functioning as experimental systems in which experiments using analytical tools from the scientific domain are enacted within the process of creation of the artwork. The results are “returned” into the artwork. These contributions are: elucidating differences in DNA helix bending and curvature along regions of gene sequences specified as either introns or exons, revealing nuanced differences in BLAST results in relation to genomics sequence metadata, and cross-correlation of astronomical data to identify putative variable signals from astronomical objects for further scientific evaluation