Literature DB >> 30387695

Data integration strategies for predictive analytics in precision medicine.

Lewis J Frey1.   

Abstract

With the rapid growth of health-related data including genomic, proteomic, imaging and clinical, the arduous task of data integration can be overwhelmed by the complexity of the environment including data size and diversity. This report examines the role of data integration strategies for big data predictive analytics in precision medicine research. Infrastructure-as-code methodologies will be discussed as a means of integrating and managing data. This includes a discussion on how and when these strategies can be used to lower barriers and address issues of consistency and interoperability within medical research environments. The goal is to support translational research and enable healthcare organizations to integrate and utilize infrastructure to accelerate the adoption of precision medicine.

Keywords:  common data models; data integration; infrastructure; infrastructure-as-code; interoperability; multiomics; precision medicine; predictive analytics; sociotechnical; virtual machines

Mesh:

Year:  2018        PMID: 30387695      PMCID: PMC6277956          DOI: 10.2217/pme-2018-0035

Source DB:  PubMed          Journal:  Per Med        ISSN: 1741-0541            Impact factor:   2.512


  19 in total

1.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.

Authors:  Aaron McKenna; Matthew Hanna; Eric Banks; Andrey Sivachenko; Kristian Cibulskis; Andrew Kernytsky; Kiran Garimella; David Altshuler; Stacey Gabriel; Mark Daly; Mark A DePristo
Journal:  Genome Res       Date:  2010-07-19       Impact factor: 9.043

2.  Toward a Taxonomy for Multi-Omics Science? Terminology Development for Whole Genome Study Approaches by Omics Technology and Hierarchy.

Authors:  Nina Pirih; Tanja Kunej
Journal:  OMICS       Date:  2017-01

3.  EHR Big Data Deep Phenotyping. Contribution of the IMIA Genomic Medicine Working Group.

Authors:  L J Frey; L Lenert; G Lopez-Campos
Journal:  Yearb Med Inform       Date:  2014-08-15

Review 4.  Representing Knowledge Consistently Across Health Systems.

Authors:  S T Rosenbloom; R J Carroll; J L Warner; M E Matheny; J C Denny
Journal:  Yearb Med Inform       Date:  2017-09-11

5.  Strategies for integrating personalized medicine into healthcare practice.

Authors:  Daryl E Pritchard; Franziska Moeckel; Mary Susan Villa; Laura T Housman; Catherine A McCarty; Howard L McLeod
Journal:  Per Med       Date:  2017-01-19       Impact factor: 2.512

Review 6.  Cloud computing for genomic data analysis and collaboration.

Authors:  Ben Langmead; Abhinav Nellore
Journal:  Nat Rev Genet       Date:  2018-01-30       Impact factor: 53.242

7.  Observational Health Data Sciences and Informatics (OHDSI): Opportunities for Observational Researchers.

Authors:  George Hripcsak; Jon D Duke; Nigam H Shah; Christian G Reich; Vojtech Huser; Martijn J Schuemie; Marc A Suchard; Rae Woong Park; Ian Chi Kei Wong; Peter R Rijnbeek; Johan van der Lei; Nicole Pratt; G Niklas Norén; Yu-Chuan Li; Paul E Stang; David Madigan; Patrick B Ryan
Journal:  Stud Health Technol Inform       Date:  2015

8.  Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images.

Authors:  Joel Saltz; Rajarsi Gupta; Le Hou; Tahsin Kurc; Pankaj Singh; Vu Nguyen; Dimitris Samaras; Kenneth R Shroyer; Tianhao Zhao; Rebecca Batiste; John Van Arnam; Ilya Shmulevich; Arvind U K Rao; Alexander J Lazar; Ashish Sharma; Vésteinn Thorsson
Journal:  Cell Rep       Date:  2018-04-03       Impact factor: 9.423

9.  Collaborative Pediatric Critical Care Research Network (CPCCRN).

Authors:  Douglas F Willson; J Michael Dean; Christopher Newth; Murray Pollack; K J S Anand; Kathleen Meert; Joseph Carcillo; Jerry Zimmerman; Carol Nicholson
Journal:  Pediatr Crit Care Med       Date:  2006-07       Impact factor: 3.624

10.  The FAIR Guiding Principles for scientific data management and stewardship.

Authors:  Mark D Wilkinson; Michel Dumontier; I Jsbrand Jan Aalbersberg; Gabrielle Appleton; Myles Axton; Arie Baak; Niklas Blomberg; Jan-Willem Boiten; Luiz Bonino da Silva Santos; Philip E Bourne; Jildau Bouwman; Anthony J Brookes; Tim Clark; Mercè Crosas; Ingrid Dillo; Olivier Dumon; Scott Edmunds; Chris T Evelo; Richard Finkers; Alejandra Gonzalez-Beltran; Alasdair J G Gray; Paul Groth; Carole Goble; Jeffrey S Grethe; Jaap Heringa; Peter A C 't Hoen; Rob Hooft; Tobias Kuhn; Ruben Kok; Joost Kok; Scott J Lusher; Maryann E Martone; Albert Mons; Abel L Packer; Bengt Persson; Philippe Rocca-Serra; Marco Roos; Rene van Schaik; Susanna-Assunta Sansone; Erik Schultes; Thierry Sengstag; Ted Slater; George Strawn; Morris A Swertz; Mark Thompson; Johan van der Lei; Erik van Mulligen; Jan Velterop; Andra Waagmeester; Peter Wittenburg; Katherine Wolstencroft; Jun Zhao; Barend Mons
Journal:  Sci Data       Date:  2016-03-15       Impact factor: 6.444

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  3 in total

1.  Informatics Ecosystems to Advance the Biology of Glycans.

Authors:  Lewis J Frey
Journal:  Methods Mol Biol       Date:  2022

2.  Metabolomic profiling reveals extensive adrenal suppression due to inhaled corticosteroid therapy in asthma.

Authors:  Priyadarshini Kachroo; Isobel D Stewart; Rachel S Kelly; Meryl Stav; Kevin Mendez; Amber Dahlin; Djøra I Soeteman; Su H Chu; Mengna Huang; Margaret Cote; Hanna M Knihtilä; Kathleen Lee-Sarwar; Michael McGeachie; Alberta Wang; Ann Chen Wu; Yamini Virkud; Pei Zhang; Nicholas J Wareham; Elizabeth W Karlson; Craig E Wheelock; Clary Clish; Scott T Weiss; Claudia Langenberg; Jessica A Lasky-Su
Journal:  Nat Med       Date:  2022-03-21       Impact factor: 87.241

3.  MALDI-MSI as a Complementary Diagnostic Tool in Cytopathology: A Pilot Study for the Characterization of Thyroid Nodules.

Authors:  Giulia Capitoli; Isabella Piga; Stefania Galimberti; Davide Leni; Angela Ida Pincelli; Mattia Garancini; Francesca Clerici; Allia Mahajneh; Virginia Brambilla; Andrew Smith; Fulvio Magni; Fabio Pagni
Journal:  Cancers (Basel)       Date:  2019-09-16       Impact factor: 6.639

  3 in total

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