Filters








25 Hits in 3.6 sec

htsget: a protocol for securely streaming genomic data

Jerome Kelleher, Mike Lin, C H Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y Gonzalez, David K Jackson, Aaron Kemp, John Marshall, Andrew Nowak (+5 others)
2018 Bioinformatics  
We have developed htsget, a protocol for secure, efficient and reliable access to sequencing read and variation data.  ...  Standardized interfaces for efficiently accessing high-throughput sequencing data are a fundamental requirement for large-scale genomic data sharing.  ...  Acknowledgements Htsget was the product of the GA4GH Streaming API task team. We acknowledge the support of the GA4GH secretariat.  ... 
doi:10.1093/bioinformatics/bty492 pmid:29931085 pmcid:PMC6298043 fatcat:slz7ksxtjffl5e7bnbfcj5t24m

D9.4 Report On Implementation Of Cloud Access And Secure User And Data Management

Dylan Spalding, Helen Parkinson, Jordi Rambla, Ilkka Lappalainen, Juha Tornroos, Alexander Senf, Thomas Keane
2018 Zenodo  
The European Genome-phenome Archive (EGA) is an ELIXIR core data resource for permanent secure archiving and sharing of all types of potentially identifiable genetic and phenotypic data resulting from  ...  In the near future, we expect that the majority of genomic data for research will come from secondary reuse of healthcare data.  ...  The EGA data access API now supports the htsget protocol.  ... 
doi:10.5281/zenodo.1452473 fatcat:kx7j2vujora47nkluvos75t6t4

CINECA Framework and APIs for executing federated genomics analyses D4.2

Alvaro Gonzalez, Shubham Kapoor, Kirill Tsukanov
2020 Zenodo  
The chosen framework supports different computing environments, which is a requirement for true federated analysis.  ...  In this deliverable, we gathered the technical requirements based on these use case descriptions and wrote a short design document which explains the requirements and lists the different options for a  ...  It is very rare to stream the data directly from the data storage archive, e.g. using the htsget streaming protocol.  ... 
doi:10.5281/zenodo.4609356 fatcat:ax4pdl4ztrdo5adoz4gxguod3q

The European Genome-phenome Archive in 2021

Mallory Ann Freeberg, Lauren A Fromont, Teresa D'Altri, Anna Foix Romero, Jorge Izquierdo Ciges, Aina Jene, Giselle Kerry, Mauricio Moldes, Roberto Ariosa, Silvia Bahena, Daniel Barrowdale, Marcos Casado Barbero (+23 others)
2021 Nucleic Acids Research  
The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting  ...  The EGA operates a distributed data access model in which requests are made to the data controller, not to the EGA, therefore, the submitter keeps control on who has access to the data and under which  ...  Additionally, the authors would like to acknowledge members of the ELIXIR Human Data Communities, the Global Alliance for Genomics and Health, the Galaxy Project, and all former and current project collaborators  ... 
doi:10.1093/nar/gkab1059 pmid:34791407 pmcid:PMC8728218 fatcat:uo5wh47terf6ve6zagmnyuoqfe

B1MG D4.1 - Secure cross-border data access roadmap - 1v0

Dylan Spalding, Tommi Nyrönen, Heikki Lehväslaiho, Riku Riski, Ilkka Lappalainen, Bengt Persson, Sergi Beltran, Regina Becker, Juan Arenas Marquez
2021 Zenodo  
A roadmap is required to communicate the plans for development of the infrastructure to provide secure cross border data access to genetic and phenotypic data to interested stakeholders.  ...  The main aim of the roadmap presented here is to define the timelines to provide a proof of concept demonstrator of secure cross border data access, describe the technologies required to develop such a  ...  htsget htsget is a data streaming protocol that allows genetic data to be securely streamed from one location to another.  ... 
doi:10.5281/zenodo.5018526 fatcat:q3zbu5t2enbhxbz7z7c3drwyd4

B1MG D4.1 - Secure cross-border data access roadmap - 1v0

Dylan Spalding, Tommi Nyrönen, Heikki Lehväslaiho, Riku Riski, Ilkka Lappalainen, Bengt Persson, Sergi Beltran, Regina Becker, Juan Arenas Marquez
2021 Zenodo  
A roadmap is required to communicate the plans for development of the infrastructure to provide secure cross border data access to genetic and phenotypic data to interested stakeholders.  ...  The main aim of the roadmap presented here is to define the timelines to provide a proof of concept demonstrator of secure cross border data access, describe the technologies required to develop such a  ...  htsget htsget is a data streaming protocol that allows genetic data to be securely streamed from one location to another.  ... 
doi:10.5281/zenodo.6139231 fatcat:42n7djpoava6dduqilw32dbobi

B1MG D4.1 - Secure cross-border data access roadmap - 1v0

Dylan Spalding, Tommi Nyrönen, Heikki Leväslaiho, Riku Riski, Ilkka Lappalainen, Bengt Persson, Sergi Beltran, Regina Becker, Juan Arenas Marquez
2021 Zenodo  
A roadmap is required to communicate the plans for development of the infrastructure to provide secure cross border data access to genetic and phenotypic data to interested stakeholders.  ...  The main aim of the roadmap presented here is to define the timelines to provide a proof of concept demonstrator of secure cross border data access, describe the technologies required to develop such a  ...  htsget htsget is a data streaming protocol that allows genetic data to be securely streamed from one location to another.  ... 
doi:10.5281/zenodo.4889401 fatcat:7ufbbxec5vdrjpjn7vjbirw54u

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Heidi L. Rehm, Angela J.H. Page, Lindsay Smith, Jeremy B. Adams, Gil Alterovitz, Lawrence J. Babb, Maxmillian P. Barkley, Michael Baudis, Michael J.S. Beauvais, Tim Beck, Jacques S. Beckmann, Sergi Beltran (+190 others)
2021 Cell Genomics  
The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and  ...  In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution.  ...  Remotely run analytical methods on data of interest htsget 12 samtools.github.io/hts- API API and tool developers, htsget is a data retrieval API that bridges from existing genomics file specs/htsget.html  ... 
doi:10.1016/j.xgen.2021.100029 pmid:35072136 pmcid:PMC8774288 fatcat:ho5hntolr5gdrlrfcgfzgah6s4

Implementation of Privacy and Security for a Genomic Information System Based on Standards

Silvia Llorente, Jaime Delgado
2022 Journal of Personalized Medicine  
such as ISO/IEC 23092 and a few GA4GH (Global Alliance for Genomics and Health) initiatives.  ...  One of the objectives of GIPAMS is to enable the management of different formats of genomic information in a unique and interoperable way, providing privacy and security for formats that do not currently  ...  Data Availability Statement: Not applicable. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/jpm12060915 pmid:35743700 pmcid:PMC9224945 fatcat:sifo7dhq4bh6fl4a5nbyytk2cy

CINECA_CanDIG and ELIXIR AAI interoperability demonstration_D2.1

Michal Procházka, Mikael Linden, Amanjeev Sethi, Thomas Binsl, Alex Michie, Mamana Mbiyavanga, Dylan Spalding
2020 Zenodo  
The interoperability covers user identification and authentication as well as the transfer of the authorisation claims following the GA4GH Passport and AAI OpenID Connect protocol (OIDC) profile specifications  ...  For controlled access, access control can be enforced for instance by the GA4GH htsget API implementation that checks the user has proper ControlledAccessGrants Visas for streaming a particular data object  ...  Tiered access to data Global Alliance for Genomics and Health (GA4GH) is promoting a three-tier access model for sensitive data: • Public access tier consists of public data.  ... 
doi:10.5281/zenodo.3938915 fatcat:arrgnz3aerhzppwasyww3l7j7y

D9.5 Report On Implementation Of Elsi And Policy Consideration For Controlled Access Data

Dylan Spalding, Jordi Rambla, Juha Törnroos, Jaakko Leinonen, Mikael Linden, Human Data Community
2018 Zenodo  
It provides technical extension to the permanent archive for all types of controlled access data, the European Genome-phenome Archive (EGA), that will support genomic information deposition, data management  ...  This report focuses on describing the improvement on the EGA processes that support the use of controlled data access protocol and compliance to the ELIXIR ELSI Policy and the European General Data Protection  ...  For example, the EXCELERATE WP9 made possible remote access from the EGA service to the Finnish ELIXIR Node secure compute environment using the new GA4GH htsget transfer protocol or accessing 11  ... 
doi:10.5281/zenodo.1452469 fatcat:corhqvmkbrgvrew43cg27sjn2m

The European Variation Archive: a FAIR resource of genomic variation for all species

Timothe Cezard, Fiona Cunningham, Sarah E Hunt, Baron Koylass, Nitin Kumar, Gary Saunders, April Shen, Andres F Silva, Kirill Tsukanov, Sundararaman Venkataraman, Paul Flicek, Helen Parkinson (+1 others)
2021 Nucleic Acids Research  
The EVA was created in 2014 to provide FAIR access to genetic variation data and has since grown to be a primary resource for genomic variants hosting >3 billion records.  ...  The European Variation Archive (EVA; https://www.ebi.ac.uk/eva/) is a resource for sharing all types of genetic variation data (SNPs, indels, and structural variants) for all species.  ...  We thank Mallory Freeberg and Jacqueline Keane for their helpful comments and feedback during the manuscript preparation.  ... 
doi:10.1093/nar/gkab960 pmid:34718739 pmcid:PMC8728205 fatcat:bz67ahna5jgh5ke53xogk5bkr4

ELIXIR-EXCELERATE D10.2: Blueprint on how to set up an ELIXIR data Node

Bengt Persson, Niclas Jareborg
2019 Zenodo  
The rapid increase in human genome sequence data, and the heterogeneous legal landscape among different countries for this type of data, makes it evident that a federated EGA organisation is the optimal  ...  This report describes how to set up a local/federated node in EGA (European Genome-phenome Archive).  ...  For supported file formats the link provides an htsget protocol encrypted data stream, which allows retrieval of whole or parts of a genome 4 sequence file.  ... 
doi:10.5281/zenodo.3381599 fatcat:7xpxrv3gereglosygq4hr6p5i4

GA4GH Passport standard for digital identity and access permissions

Craig Voisin, Mikael Linden, Stephanie O.M. Dyke, Sarion R. Bowers, Pinar Alper, Maxmillian P. Barkley, David Bernick, Jianpeng Chao, Mélanie Courtot, Francis Jeanson, Melissa A. Konopko, Martin Kuba (+12 others)
2021 Cell Genomics  
Highlights d The GA4GH Passport is an open standard to encode data access permissions of users d The standard enables communication of data access permissions at international scale d Passport facilitates  ...  data access and analysis across international platforms d Implementers include research initiatives, infrastructures, and national institutes  ...  Many other GA4GH standards describe APIs for programmatic access to sensitive data and services, such as Beacon API for data discovery, htsget API for data streaming, and WES 1 for remote execution of  ... 
doi:10.1016/j.xgen.2021.100030 fatcat:idfx5dtwhncbtdzurl5at47t4m

CINECA Data Management Plan v2

Leslie Glass, Dylan Spalding, Nicola Mulder, Melanie Courtot, Fiona Brinkman, Patrick Ruch
2021 Zenodo  
Given the international nature of this project, the data management plan is a component of Work Package 7 - Ethical and legal governance framework for transnational data-sharing.  ...  All data access is determined by the existing data access committees (DACs) and the respective data processes for each dataset (Appendix 1 explains the process for accessing secondary use data for each  ...  Alignment of CINECA with GA4GH will ensure that access and interoperability can be achieved using community tools, e.g. the htsget API for streaming and accessing genomic 14 data has been implemented by  ... 
doi:10.5281/zenodo.4683415 fatcat:csk7c3iehfce7kotsdoxulm2ta
« Previous Showing results 1 — 15 out of 25 results