Literature DB >> 28501646

Developing a framework for digital objects in the Big Data to Knowledge (BD2K) commons: Report from the Commons Framework Pilots workshop.

Kathleen M Jagodnik1, Simon Koplev1, Sherry L Jenkins1, Lucila Ohno-Machado2, Benedict Paten3, Stephan C Schurer4, Michel Dumontier5, Ruben Verborgh6, Alex Bui7, Peipei Ping8, Neil J McKenna9, Ravi Madduri10, Ajay Pillai11, Avi Ma'ayan12.   

Abstract

The volume and diversity of data in biomedical research have been rapidly increasing in recent years. While such data hold significant promise for accelerating discovery, their use entails many challenges including: the need for adequate computational infrastructure, secure processes for data sharing and access, tools that allow researchers to find and integrate diverse datasets, and standardized methods of analysis. These are just some elements of a complex ecosystem that needs to be built to support the rapid accumulation of these data. The NIH Big Data to Knowledge (BD2K) initiative aims to facilitate digitally enabled biomedical research. Within the BD2K framework, the Commons initiative is intended to establish a virtual environment that will facilitate the use, interoperability, and discoverability of shared digital objects used for research. The BD2K Commons Framework Pilots Working Group (CFPWG) was established to clarify goals and work on pilot projects that address existing gaps toward realizing the vision of the BD2K Commons. This report reviews highlights from a two-day meeting involving the BD2K CFPWG to provide insights on trends and considerations in advancing Big Data science for biomedical research in the United States.
Copyright © 2017 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Accessibility; Big Data; FAIR principles; Findability; Interoperability; Reusability

Mesh:

Year:  2017        PMID: 28501646      PMCID: PMC5545976          DOI: 10.1016/j.jbi.2017.05.006

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  34 in total

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2.  May the best analyst win.

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3.  The NIH BD2K center for big data in translational genomics.

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Journal:  J Am Med Inform Assoc       Date:  2015-07-13       Impact factor: 4.497

4.  The global alliance for genomics & health.

Authors:  Sharon F Terry
Journal:  Genet Test Mol Biomarkers       Date:  2014-06

Review 5.  Predictive, personalized, preventive, participatory (P4) cancer medicine.

Authors:  Leroy Hood; Stephen H Friend
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Review 6.  Harnessing Big Data for Systems Pharmacology.

Authors:  Lei Xie; Eli J Draizen; Philip E Bourne
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7.  Crowdsourcing network inference: the DREAM predictive signaling network challenge.

Authors:  Robert J Prill; Julio Saez-Rodriguez; Leonidas G Alexopoulos; Peter K Sorger; Gustavo Stolovitzky
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8.  The Online Bioinformatics Resources Collection at the University of Pittsburgh Health Sciences Library System--a one-stop gateway to online bioinformatics databases and software tools.

Authors:  Yi-Bu Chen; Ansuman Chattopadhyay; Phillip Bergen; Cynthia Gadd; Nancy Tannery
Journal:  Nucleic Acids Res       Date:  2006-11-15       Impact factor: 16.971

9.  The National Institutes of Health's Big Data to Knowledge (BD2K) initiative: capitalizing on biomedical big data.

Authors:  Ronald Margolis; Leslie Derr; Michelle Dunn; Michael Huerta; Jennie Larkin; Jerry Sheehan; Mark Guyer; Eric D Green
Journal:  J Am Med Inform Assoc       Date:  2014-07-09       Impact factor: 4.497

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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  13 in total

Review 1.  Progress in data interoperability to support computational toxicology and chemical safety evaluation.

Authors:  Sean Watford; Stephen Edwards; Michelle Angrish; Richard S Judson; Katie Paul Friedman
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Review 2.  Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome: Where There Is a Will, There Is a Way.

Authors:  Justyna Fert-Bober; Christopher I Murray; Sarah J Parker; Jennifer E Van Eyk
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

3.  Data Dissemination: Shortening the Long Tail of Traumatic Brain Injury Dark Data.

Authors:  Bridget E Hawkins; J Russell Huie; Carlos Almeida; Jiapei Chen; Adam R Ferguson
Journal:  J Neurotrauma       Date:  2019-03-29       Impact factor: 5.269

4.  Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses.

Authors:  Denis Torre; Patrycja Krawczuk; Kathleen M Jagodnik; Alexander Lachmann; Zichen Wang; Lily Wang; Maxim V Kuleshov; Avi Ma'ayan
Journal:  Sci Data       Date:  2018-02-27       Impact factor: 8.501

5.  Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center.

Authors:  Vasileios Stathias; Amar Koleti; Dušica Vidović; Daniel J Cooper; Kathleen M Jagodnik; Raymond Terryn; Michele Forlin; Caty Chung; Denis Torre; Nagi Ayad; Mario Medvedovic; Avi Ma'ayan; Ajay Pillai; Stephan C Schürer
Journal:  Sci Data       Date:  2018-06-19       Impact factor: 6.444

Review 6.  Translational bioinformatics in mental health: open access data sources and computational biomarker discovery.

Authors:  Jessica D Tenenbaum; Krithika Bhuvaneshwar; Jane P Gagliardi; Kate Fultz Hollis; Peilin Jia; Liang Ma; Radhakrishnan Nagarajan; Gopalkumar Rakesh; Vignesh Subbian; Shyam Visweswaran; Zhongming Zhao; Leon Rozenblit
Journal:  Brief Bioinform       Date:  2019-05-21       Impact factor: 11.622

7.  Long-term preservation of biomedical research data.

Authors:  Vivek Navale; Matthew McAuliffe
Journal:  F1000Res       Date:  2018-08-29

8.  Cloud computing applications for biomedical science: A perspective.

Authors:  Vivek Navale; Philip E Bourne
Journal:  PLoS Comput Biol       Date:  2018-06-14       Impact factor: 4.475

9.  Protecting User Privacy and Rights in Academic Data-Sharing Partnerships: Principles From a Pilot Program at Crisis Text Line.

Authors:  Anthony R Pisani; Nitya Kanuri; Bob Filbin; Carlos Gallo; Madelyn Gould; Lisa Soleymani Lehmann; Robert Levine; John E Marcotte; Brian Pascal; David Rousseau; Shairi Turner; Shirley Yen; Megan L Ranney
Journal:  J Med Internet Res       Date:  2019-01-17       Impact factor: 5.428

10.  Identification of Liver Cancer Stem Cell Stemness Markers Using a Comparative Analysis of Public Data Sets.

Authors:  Kirill Borziak; Joseph Finkelstein
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