Literature DB >> 29033693

A Case for Data Commons: Toward Data Science as a Service.

Robert L Grossman1, Allison Heath1, Mark Murphy1, Maria Patterson1, Walt Wells2.   

Abstract

Data commons collocate data, storage, and computing infrastructure with core services and commonly used tools and applications for managing, analyzing, and sharing data to create an interoperable resource for the research community. An architecture for data commons is described, as well as some lessons learned from operating several large-scale data commons.

Entities:  

Year:  2016        PMID： 29033693      PMCID： PMC5636009          DOI： 10.1109/MCSE.2016.92

Source DB:  PubMed          Journal:  Comput Sci Eng        ISSN： 1521-9615            Impact factor:   2.080


  3 in total

1.  Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

Authors:  Allison P Heath; Matthew Greenway; Raymond Powell; Jonathan Spring; Rafael Suarez; David Hanley; Chai Bandlamudi; Megan E McNerney; Kevin P White; Robert L Grossman
Journal:  J Am Med Inform Assoc       Date:  2014-01-24       Impact factor: 4.497

2.  Data use under the NIH GWAS data sharing policy and future directions.

Authors:  Dina N Paltoo; Laura Lyman Rodriguez; Michael Feolo; Elizabeth Gillanders; Erin M Ramos; Joni L Rutter; Stephen Sherry; Vivian Ota Wang; Alice Bailey; Rebecca Baker; Mark Caulder; Emily L Harris; Kristofor Langlais; Hilary Leeds; Erin Luetkemeier; Taunton Paine; Tamar Roomian; Kimberly Tryka; Amy Patterson; Eric D Green
Journal:  Nat Genet       Date:  2014-09       Impact factor: 38.330

3.  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
  3 in total
  16 in total

Review 1.  Progress Toward Cancer Data Ecosystems.

Authors:  Robert L Grossman
Journal:  Cancer J       Date:  2018 May/Jun       Impact factor: 3.360

2.  Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.

Authors:  Shane Wilson; Michael Fitzsimons; Martin Ferguson; Allison Heath; Mark Jensen; Josh Miller; Mark W Murphy; James Porter; Himanso Sahni; Louis Staudt; Yajing Tang; Zhining Wang; Christine Yu; Junjun Zhang; Vincent Ferretti; Robert L Grossman
Journal:  Cancer Res       Date:  2017-11-01       Impact factor: 12.701

Review 3.  Artificial Intelligence for Precision Oncology.

Authors:  Sherry Bhalla; Alessandro Laganà
Journal:  Adv Exp Med Biol       Date:  2022       Impact factor: 2.622

4.  Economical Utilization of Health Information with Learning Healthcare System Data Commons.

Authors:  Thomas O'Hara; Anil Saldanha; Matthew Trunnell; Robert L Grossman; Bala Hota; Casey Frankenberger
Journal:  Perspect Health Inf Manag       Date:  2022-03-15

5.  New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx.

Authors:  Mohamed Mounir; Marta Lucchetta; Tiago C Silva; Catharina Olsen; Gianluca Bontempi; Xi Chen; Houtan Noushmehr; Antonio Colaprico; Elena Papaleo
Journal:  PLoS Comput Biol       Date:  2019-03-05       Impact factor: 4.475

Review 6.  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

7.  NCI Imaging Data Commons.

Authors:  Andrey Fedorov; William J R Longabaugh; David Pot; David A Clunie; Steve Pieper; Hugo J W L Aerts; André Homeyer; Rob Lewis; Afshin Akbarzadeh; Dennis Bontempi; William Clifford; Markus D Herrmann; Henning Höfener; Igor Octaviano; Chad Osborne; Suzanne Paquette; James Petts; Davide Punzo; Madelyn Reyes; Daniela P Schacherer; Mi Tian; George White; Erik Ziegler; Ilya Shmulevich; Todd Pihl; Ulrike Wagner; Keyvan Farahani; Ron Kikinis
Journal:  Cancer Res       Date:  2021-06-15       Impact factor: 12.701

Review 8.  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

9.  Differential expression of receptors mediating receptor-mediated transcytosis (RMT) in brain microvessels, brain parenchyma and peripheral tissues of the mouse and the human.

Authors:  Wandong Zhang; Qing Yan Liu; Arsalan S Haqqani; Sonia Leclerc; Ziying Liu; François Fauteux; Ewa Baumann; Christie E Delaney; Dao Ly; Alexandra T Star; Eric Brunette; Caroline Sodja; Melissa Hewitt; Jagdeep K Sandhu; Danica B Stanimirovic
Journal:  Fluids Barriers CNS       Date:  2020-07-22

10.  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
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