Literature DB >> 29794537

Progress Toward Cancer Data Ecosystems.

Robert L Grossman1.   

Abstract

One of the recommendations of the Cancer Moonshot Blue Ribbon Panel report from 2016 was the creation of a national cancer data ecosystem. We review some of the approaches for building cancer data ecosystems and some of the progress that has been made. A data commons is the colocation of data with cloud computing infrastructure and commonly used software services, tools, and applications for managing, integrating, analyzing, and sharing data to create an interoperable resource for the research community. We discuss data commons and their potential role in cancer data ecosystems and, in particular, how multiple data commons can interoperate to form part of the foundation for a cancer data ecosystem.

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Year:  2018        PMID: 29794537      PMCID: PMC5988431          DOI: 10.1097/PPO.0000000000000318

Source DB:  PubMed          Journal:  Cancer J        ISSN: 1528-9117            Impact factor:   3.360


  33 in total

Review 1.  A survey of current trends in computational drug repositioning.

Authors:  Jiao Li; Si Zheng; Bin Chen; Atul J Butte; S Joshua Swamidass; Zhiyong Lu
Journal:  Brief Bioinform       Date:  2015-03-31       Impact factor: 11.622

Review 2.  Data Commons to Support Pediatric Cancer Research.

Authors:  Samuel L Volchenboum; Suzanne M Cox; Allison Heath; Adam Resnick; Susan L Cohn; Robert Grossman
Journal:  Am Soc Clin Oncol Educ Book       Date:  2017

3.  The Human Cell Atlas: from vision to reality.

Authors:  Orit Rozenblatt-Rosen; Michael J T Stubbington; Aviv Regev; Sarah A Teichmann
Journal:  Nature       Date:  2017-10-18       Impact factor: 49.962

4.  The Cancer Genomics Cloud: Collaborative, Reproducible, and Democratized-A New Paradigm in Large-Scale Computational Research.

Authors:  Jessica W Lau; Erik Lehnert; Anurag Sethi; Raunaq Malhotra; Gaurav Kaushik; Zeynep Onder; Nick Groves-Kirkby; Aleksandar Mihajlovic; Jack DiGiovanna; Mladen Srdic; Dragan Bajcic; Jelena Radenkovic; Vladimir Mladenovic; Damir Krstanovic; Vladan Arsenijevic; Djordje Klisic; Milan Mitrovic; Igor Bogicevic; Deniz Kural; Brandi Davis-Dusenbery
Journal:  Cancer Res       Date:  2017-11-01       Impact factor: 12.701

5.  Toward a Shared Vision for Cancer Genomic Data.

Authors:  Robert L Grossman; Allison P Heath; Vincent Ferretti; Harold E Varmus; Douglas R Lowy; Warren A Kibbe; Louis M Staudt
Journal:  N Engl J Med       Date:  2016-09-22       Impact factor: 91.245

6.  Building a rapid learning health care system for oncology: the regulatory framework of CancerLinQ.

Authors:  Richard L Schilsky; Dina L Michels; Amy H Kearbey; Peter Paul Yu; Clifford A Hudis
Journal:  J Clin Oncol       Date:  2014-06-09       Impact factor: 44.544

7.  All the World's a Stage: Facilitating Discovery Science and Improved Cancer Care through the Global Alliance for Genomics and Health.

Authors:  Mark Lawler; Lillian L Siu; Heidi L Rehm; Stephen J Chanock; Gil Alterovitz; John Burn; Fabien Calvo; Denis Lacombe; Bin Tean Teh; Kathryn N North; Charles L Sawyers
Journal:  Cancer Discov       Date:  2015-11       Impact factor: 39.397

8.  Inexpensive and Highly Reproducible Cloud-Based Variant Calling of 2,535 Human Genomes.

Authors:  Suyash S Shringarpure; Andrew Carroll; Francisco M De La Vega; Carlos D Bustamante
Journal:  PLoS One       Date:  2015-06-25       Impact factor: 3.240

9.  ClinVar: public archive of relationships among sequence variation and human phenotype.

Authors:  Melissa J Landrum; Jennifer M Lee; George R Riley; Wonhee Jang; Wendy S Rubinstein; Deanna M Church; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2013-11-14       Impact factor: 16.971

10.  A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine.

Authors:  Izumi V Hinkson; Tanja M Davidsen; Juli D Klemm; Anthony R Kerlavage; Warren A Kibbe; Ishwar Chandramouliswaran
Journal:  Front Cell Dev Biol       Date:  2017-09-21
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  5 in total

1.  The National Cancer Institute's Role in Advancing Health-Care Delivery Research.

Authors:  Paul B Jacobsen; Janet de Moor; V Paul Doria-Rose; Ann M Geiger; Sarah C Kobrin; Annie Sampson; Ashley Wilder Smith
Journal:  J Natl Cancer Inst       Date:  2022-01-11       Impact factor: 13.506

Review 2.  Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data.

Authors:  Robert L Grossman
Journal:  Trends Genet       Date:  2019-01-25       Impact factor: 11.639

3.  From biomedical cloud platforms to microservices: next steps in FAIR data and analysis.

Authors:  Nathan C Sheffield; Vivien R Bonazzi; Philip E Bourne; Tony Burdett; Timothy Clark; Robert L Grossman; Ola Spjuth; Andrew D Yates
Journal:  Sci Data       Date:  2022-09-08       Impact factor: 8.501

4.  Insights from Adopting a Data Commons Approach for Large-scale Observational Cohort Studies: The California Teachers Study.

Authors:  James V Lacey; Nadia T Chung; Paul Hughes; Jennifer L Benbow; Christine Duffy; Kristen E Savage; Emma S Spielfogel; Sophia S Wang; Maria Elena Martinez; Sandeep Chandra
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2020-02-12       Impact factor: 4.254

Review 5.  Using big data in pediatric oncology: Current applications and future directions.

Authors:  Ajay Major; Suzanne M Cox; Samuel L Volchenboum
Journal:  Semin Oncol       Date:  2020-02-29       Impact factor: 5.385

  5 in total

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