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DataSHIELD – New Directions and Dimensions

Rebecca C. Wilson, Oliver W. Butters, Demetris Avraam, James Baker, Jonathan A. Tedds, Andrew Turner, Madeleine Murtagh, Paul R. Burton
2017 Data Science Journal  
This paper reports three new applications of DataSHIELD including application to post-publication sensitive data analysis, text data analysis and privacy protected data visualisation.  ...  Expansion of DataSHIELD analytic functionality and application to additional data types demonstrate the broad applications of the software beyond biomedical sciences.  ...  Acknowledgements We thank the BioSHaRE-EU consortium for their involvement in the DataSHIELD pilots; F1000Research and the British Library for providing sample datasets and the active DataSHIELD development  ... 
doi:10.5334/dsj-2017-021 fatcat:lc4i2vtfzrcf5drqxae4td7xb4

Deep generative models in DataSHIELD [article]

Stefan Lenz, Harald Binder
2020 arXiv   pre-print
The DataSHIELD software provides an infrastructure and a set of statistical methods for joint analyses of distributed data.  ...  For the implementation, we employ the package "BoltzmannMachines" from the Julia programming language and wrap it for use with DataSHIELD, which is based on R.  ...  Acknowledgements This work has been supported by the Federal Ministry of Education and Research (BMBF) in Germany in the MIRACUM project (FKZ 01ZZ1801B).  ... 
arXiv:2003.07775v1 fatcat:f6a6b3vjezblddc6gbaermcflq

Deep generative models in DataSHIELD

Stefan Lenz, Moritz Hess, Harald Binder
2021 BMC Medical Research Methodology  
Methods The DataSHIELD software provides an infrastructure and a set of statistical methods for joint, privacy-preserving analyses of distributed data.  ...  For the implementation, we use the package "BoltzmannMachines" from the Julia programming language and wrap it for use with DataSHIELD, which is based on R.  ...  Authors' contributions HB and SL developed the concept for the analysis and the simulation design. SL designed and implemented the software and conducted the analyses.  ... 
doi:10.1186/s12874-021-01237-6 pmid:33812380 fatcat:yqfivrotdff5fayvpgxwkeze6q

Orchestrating privacy-protected big data analyses of data from different resources with R and DataSHIELD

Yannick Marcon, Tom Bishop, Demetris Avraam, Xavier Escriba-Montagut, Patricia Ryser-Welch, Stuart Wheater, Paul Burton, Juan R. González, Dina Schneidman-Duhovny
2021 PLoS Computational Biology  
We present a new architecture ("resources") for DataSHIELD and Opal to allow large, complex datasets to be used at their original location, in their original format and with external computing facilities  ...  However, until now the analysis of big data with DataSHIELD has been limited by the storage formats available in Opal and the analysis capabilities available in the DataSHIELD R packages.  ...  Acknowledgments We would like to thank the software developers and scientific staff who have worked on Opal.  ... 
doi:10.1371/journal.pcbi.1008880 pmid:33784300 fatcat:thhhk5smhbhl5ns62w2ydzldya

DataSHIELD: resolving a conflict in contemporary bioscience--performing a pooled analysis of individual-level data without sharing the data

M. Wolfson, S. E. Wallace, N. Masca, G. Rowe, N. A. Sheehan, V. Ferretti, P. LaFlamme, M. D. Tobin, J. Macleod, J. Little, I. Fortier, B. M. Knoppers (+1 others)
2010 International Journal of Epidemiology  
Results The conceptual use of DataSHIELD is illustrated in two different settings.  ...  Methods Data aggregation through anonymous summary-statistics from harmonized individual-level databases (DataSHIELD), provides a simple approach to analysing pooled data that circumvents this conflict  ...  responded cautiously to these concerns, ensuring that all ethico-legal stipulations are met and that new issues are dealt with carefully, as and when they arise. 23, 27 Given this caution, it is perhaps  ... 
doi:10.1093/ije/dyq111 pmid:20630989 pmcid:PMC2972441 fatcat:m45kwgzhw5berdntot5kg2wh44

Cohort description: Measures of early-life behaviour and later psychopathology in the LifeCycle Project - EU Child Cohort Network

Johanna L. Nader, Mònica López-Vicente, Jordi Julvez, Monica Guxens, Tim Cadman, Ahmed Elhakeem, Marjo-Riitta Järvelin, Nina Rautio, Jouko Miettunen, Hanan El Marroun, Maria Melchior, Barbara Heude (+26 others)
2021 Journal of Epidemiology  
The mental health data in LifeCycle contain longitudinal and cross-sectional data for ages 0-18+ years, covering domains across a wide range of behavioural and psychopathology indicators and outcomes (  ...  including executive function, depression, ADHD and cognition).  ...  The long-term dedication and commitment of both the staff and participants involved in these studies have made this work possible.  ... 
doi:10.2188/jea.je20210241 pmid:34776498 fatcat:hfmj5qycn5e2lnbikh2qdcqv4m

Integrative High Dimensional Multiple Testing with Heterogeneity under Data Sharing Constraints [article]

Molei Liu, Yin Xia, Kelly Cho, Tianxi Cai
2020 arXiv   pre-print
Simulation studies demonstrate that the DSILT procedure performs well in both false discovery control and attaining power.  ...  Identifying informative predictors in a high dimensional regression model is a critical step for association analysis and predictive modeling.  ...  The covariate vector X = (X T main , X T int ) T is of dimension p = 516, where X main consists of the main effects of rs17238484, age and the aforementioned 256 SNPs, and X int consists of the interactions  ... 
arXiv:2004.00816v3 fatcat:dx25d32bj5cmll6spnlc6xojze

CanDIG: Secure Federated Genomic Queries and Analyses Across Jurisdictions [article]

Lewis Jonathan Dursi, Zoltan Bozoky, Richard de Borja, Jimmy Li, David Bujold, Adam Lipski, Shaikh Farhan Rashid, Amanjeev Sethi, Neelam Memon, Dashaylan Naidoo, Felipe Coral-Sasso, Matthew Wong (+19 others)
2021 bioRxiv   pre-print
in the clinic and the laboratory.  ...  Rapid expansions of bioinformatics and computational biology have broadened the collection and use of -omics data including genomic, transcriptomic, methylomic and a myriad of other health data types,  ...  Initial pushes towards interoperability and federation are driving new efforts and solutions (Birney et al., 2017) .  ... 
doi:10.1101/2021.03.30.434101 fatcat:y6g4ic2pafghjnutw6rbyotuyq

D8.2 Overview Document on Already Existing Data Harmonisation Tools

Sebastian Mate, Ines Leb, Christina Schüttler, Kaisa Silander, Timo Miettinen, Juha Knuuttila, Niina Eklund, Hans-Ulrich Prokosch
2016 Zenodo  
In addition, it will include information on the different levels and versions of various standardised and non-standardised ontologies and data dictionaries and schemas.  ...  The aim of this document is to analyse the state of the art and existing tools for data harmonisation, considering their applicability within CS-IT.  ...  /), which however, does not seem to al-low searches on a direct sample level.  ... 
doi:10.5281/zenodo.165775 fatcat:gv3654h5ondpri6hbuo2hdppeq

Dietary Patterns Are Associated with Serum Metabolite Patterns and Their Association Is Influenced by Gut Bacteria among Older German Adults

2019 Journal of Nutrition  
We modeled associations between DPs and 8 previously published MPs and the modifying effect of BCPs by fitting generalized linear models using DataSHIELD R. We identified 5 DPs and 7 BCPs.  ...  The "bread, margarine, and processed meat" and "fruiting vegetables and vegetable oils" DPs were positively associated with the "amino acids" (β = 0.35; 95% CI: 0.02, 0.69; P = 0.03) and "fatty acids"  ...  ; KO: analyzed and interpreted the data and wrote the manuscript; and all authors: revised the manuscript and read and approved the final manuscript.  ... 
doi:10.1093/jn/nxz194 pmid:31504715 pmcid:PMC6946898 fatcat:fwnxg3vakjachdkzxjk7usobq4

Privacy-preserving data sharing infrastructures for medical research: systematization and comparison

Felix Nikolaus Wirth, Thierry Meurers, Marco Johns, Fabian Prasser
2021 BMC Medical Informatics and Decision Making  
As a result, various approaches and infrastructures have been developed that aim to ensure that patients and research participants remain anonymous when data is shared.  ...  Based on this contribution, we categorized popular data sharing approaches and identified research gaps by analyzing combinations of promising properties and features that are not yet supported by existing  ...  dimensions.  ... 
doi:10.1186/s12911-021-01602-x fatcat:7xrq26aowvcsbfrkw2ot5u5ceu

COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and Processing Decentralized Brain Imaging Data

Sergey M. Plis, Anand D. Sarwate, Dylan Wood, Christopher Dieringer, Drew Landis, Cory Reed, Sandeep R. Panta, Jessica A. Turner, Jody M. Shoemaker, Kim W. Carter, Paul Thompson, Kent Hutchison (+1 others)
2016 Frontiers in Neuroscience  
Data sharing mandates from public funding agencies and major journal publishers have spurred the development of data repositories and neuroinformatics consortia.  ...  The field of neuroimaging has embraced the need for sharing and collaboration.  ...  new collaborations/consortia within the system.  ... 
doi:10.3389/fnins.2016.00365 pmid:27594820 pmcid:PMC4990563 fatcat:7phqdhwhobgydc7rs3og64jc5y

SCOR: A secure international informatics infrastructure to investigate COVID-19

J L Raisaro, Francesco Marino, Juan Troncoso-Pastoriza, Raphaelle Beau-Lejdstrom, Riccardo Bellazzi, Robert Murphy, Elmer V Bernstam, Henry Wang, Mauro Bucalo, Yong Chen, Assaf Gottlieb, Arif Harmanci (+22 others)
2020 JAMIA Journal of the American Medical Informatics Association  
Global pandemics call for large and diverse healthcare data to study various risk factors, treatment options, and disease progression patterns.  ...  We hope our effort will make a change and accelerate research in future pandemics with broad and diverse samples on an international scale.  ...  COVID-19 research moves rapidly with new initiatives announced daily.  ... 
doi:10.1093/jamia/ocaa172 pmid:32918447 pmcid:PMC7454652 fatcat:kol6vnbybvaz5i4sca322kcy4e

Is there a role for statistics in artificial intelligence?

Sarah Friedrich, Gerd Antes, Sigrid Behr, Harald Binder, Werner Brannath, Florian Dumpert, Katja Ickstadt, Hans A. Kestler, Johannes Lederer, Heinz Leitgöb, Markus Pauly, Ansgar Steland (+2 others)
2021 Advances in Data Analysis and Classification  
collection, differentiation of causality and associations and assessment of uncertainty in results.  ...  AbstractThe research on and application of artificial intelligence (AI) has triggered a comprehensive scientific, economic, social and political discussion.  ...  Moreover, Willi Sauerbrei (University Freiburg) and Kaspar Rufibach (F. Hoffmann-La Roche Ltd) provided valuable comments.  ... 
doi:10.1007/s11634-021-00455-6 fatcat:xwuoyg6l3jcejcvqfsmhrvpzvm

Behavior Genetics Association 43rd Annual Meeting Abstracts

2013 Behavior Genetics  
Factor analysis singled out 2 factors: 1) the dependence on the circumstances and the inability to cope with changing conditions, 2) planning and persistence.  ...  They were genotyped for polymorphisms of 2 genes (a serotonin transporter gene promoter polymorphism (5 HTTLPR) and serotonin 2C receptor (5 HT2CR)) and filled in several questionnaires.  ...  Comparative design across populations will create a totally new dimension for the study, and thus this consortium creates opportunity for a large number of comprehensive research papers using a very limited  ... 
doi:10.1007/s10519-013-9623-9 fatcat:fvi46ghgtrcbvk2lzp54zive5y
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