Translational research platforms integrating clinical and omics data: a review of publicly available solutions

The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms al...

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Main Authors:	Canuel, Vincent, Rance, Bastien, Avillach, Paul, Degoulet, Patrice, Burgun, Anita
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364065/

id	pubmed-4364065
recordtype	oai_dc
spelling	pubmed-43640652015-03-25 Translational research platforms integrating clinical and omics data: a review of publicly available solutions Canuel, Vincent Rance, Bastien Avillach, Paul Degoulet, Patrice Burgun, Anita Papers The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features. Oxford University Press 2015-03 2014-03-07 /pmc/articles/PMC4364065/ /pubmed/24608524 http://dx.doi.org/10.1093/bib/bbu006 Text en © The Author 2014. Published by Oxford University Press. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Canuel, Vincent Rance, Bastien Avillach, Paul Degoulet, Patrice Burgun, Anita
spellingShingle	Canuel, Vincent Rance, Bastien Avillach, Paul Degoulet, Patrice Burgun, Anita Translational research platforms integrating clinical and omics data: a review of publicly available solutions
author_facet	Canuel, Vincent Rance, Bastien Avillach, Paul Degoulet, Patrice Burgun, Anita
author_sort	Canuel, Vincent
title	Translational research platforms integrating clinical and omics data: a review of publicly available solutions
title_short	Translational research platforms integrating clinical and omics data: a review of publicly available solutions
title_full	Translational research platforms integrating clinical and omics data: a review of publicly available solutions
title_fullStr	Translational research platforms integrating clinical and omics data: a review of publicly available solutions
title_full_unstemmed	Translational research platforms integrating clinical and omics data: a review of publicly available solutions
title_sort	translational research platforms integrating clinical and omics data: a review of publicly available solutions
description	The rise of personalized medicine and the availability of high-throughput molecular analyses in the context of clinical care have increased the need for adequate tools for translational researchers to manage and explore these data. We reviewed the biomedical literature for translational platforms allowing the management and exploration of clinical and omics data, and identified seven platforms: BRISK, caTRIP, cBio Cancer Portal, G-DOC, iCOD, iDASH and tranSMART. We analyzed these platforms along seven major axes. (1) The community axis regrouped information regarding initiators and funders of the project, as well as availability status and references. (2) We regrouped under the information content axis the nature of the clinical and omics data handled by each system. (3) The privacy management environment axis encompassed functionalities allowing control over data privacy. (4) In the analysis support axis, we detailed the analytical and statistical tools provided by the platforms. We also explored (5) interoperability support and (6) system requirements. The final axis (7) platform support listed the availability of documentation and installation procedures. A large heterogeneity was observed in regard to the capability to manage phenotype information in addition to omics data, their security and interoperability features. The analytical and visualization features strongly depend on the considered platform. Similarly, the availability of the systems is variable. This review aims at providing the reader with the background to choose the platform best suited to their needs. To conclude, we discuss the desiderata for optimal translational research platforms, in terms of privacy, interoperability and technical features.
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4364065/
_version_	1613200137346088960

Translational research platforms integrating clinical and omics data: a review of publicly available solutions

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