Literature DB >> 22281772

Toward interoperable bioscience data.

Susanna-Assunta Sansone1, Philippe Rocca-Serra, Dawn Field, Eamonn Maguire, Chris Taylor, Oliver Hofmann, Hong Fang, Steffen Neumann, Weida Tong, Linda Amaral-Zettler, Kimberly Begley, Tim Booth, Lydie Bougueleret, Gully Burns, Brad Chapman, Tim Clark, Lee-Ann Coleman, Jay Copeland, Sudeshna Das, Antoine de Daruvar, Paula de Matos, Ian Dix, Scott Edmunds, Chris T Evelo, Mark J Forster, Pascale Gaudet, Jack Gilbert, Carole Goble, Julian L Griffin, Daniel Jacob, Jos Kleinjans, Lee Harland, Kenneth Haug, Henning Hermjakob, Shannan J Ho Sui, Alain Laederach, Shaoguang Liang, Stephen Marshall, Annette McGrath, Emily Merrill, Dorothy Reilly, Magali Roux, Caroline E Shamu, Catherine A Shang, Christoph Steinbeck, Anne Trefethen, Bryn Williams-Jones, Katherine Wolstencroft, Ioannis Xenarios, Winston Hide.   

Abstract

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision.

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Year:  2012        PMID: 22281772      PMCID: PMC3428019          DOI: 10.1038/ng.1054

Source DB:  PubMed          Journal:  Nat Genet        ISSN: 1061-4036            Impact factor:   38.330


  27 in total

1.  Credit where credit is overdue.

Authors: 
Journal:  Nat Biotechnol       Date:  2009-07       Impact factor: 54.908

2.  Data sharing: Empty archives.

Authors:  Bryn Nelson
Journal:  Nature       Date:  2009-09-10       Impact factor: 49.962

Review 3.  Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery.

Authors:  Michael R Barnes; Lee Harland; Steven M Foord; Matthew D Hall; Ian Dix; Scott Thomas; Bryn I Williams-Jones; Cory R Brouwer
Journal:  Nat Rev Drug Discov       Date:  2009-07-17       Impact factor: 84.694

4.  Accreditation and attribution in data sharing.

Authors:  Gudmundur A Thorisson
Journal:  Nat Biotechnol       Date:  2009-11       Impact factor: 54.908

5.  Advancing regulatory science.

Authors:  Margaret A Hamburg
Journal:  Science       Date:  2011-02-25       Impact factor: 47.728

6.  Dealing with data. Challenges and opportunities. Introduction.

Authors: 
Journal:  Science       Date:  2011-02-11       Impact factor: 47.728

7.  Sharing and archiving nucleic acid structure mapping data.

Authors:  Philippe Rocca-Serra; Stanislav Bellaousov; Amanda Birmingham; Chunxia Chen; Pablo Cordero; Rhiju Das; Lauren Davis-Neulander; Caia D S Duncan; Matthew Halvorsen; Rob Knight; Neocles B Leontis; David H Mathews; Justin Ritz; Jesse Stombaugh; Kevin M Weeks; Craig L Zirbel; Alain Laederach
Journal:  RNA       Date:  2011-05-24       Impact factor: 4.942

8.  NCBI GEO: archive for high-throughput functional genomic data.

Authors:  Tanya Barrett; Dennis B Troup; Stephen E Wilhite; Pierre Ledoux; Dmitry Rudnev; Carlos Evangelista; Irene F Kim; Alexandra Soboleva; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Rolf N Muertter; Ron Edgar
Journal:  Nucleic Acids Res       Date:  2008-10-21       Impact factor: 16.971

9.  Big data: The future of biocuration.

Authors:  Doug Howe; Maria Costanzo; Petra Fey; Takashi Gojobori; Linda Hannick; Winston Hide; David P Hill; Renate Kania; Mary Schaeffer; Susan St Pierre; Simon Twigger; Owen White; Seung Yon Rhee
Journal:  Nature       Date:  2008-09-04       Impact factor: 49.962

10.  Post-publication sharing of data and tools.

Authors:  Paul N Schofield; Tania Bubela; Thomas Weaver; Lili Portilla; Stephen D Brown; John M Hancock; David Einhorn; Glauco Tocchini-Valentini; Martin Hrabe de Angelis; Nadia Rosenthal
Journal:  Nature       Date:  2009-09-10       Impact factor: 49.962

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  148 in total

1.  My data are your data.

Authors:  Vivien Marx
Journal:  Nat Biotechnol       Date:  2012-06-07       Impact factor: 54.908

2.  Developing a data element repository to support EHR-driven phenotype algorithm authoring and execution.

Authors:  Guoqian Jiang; Richard C Kiefer; Luke V Rasmussen; Harold R Solbrig; Huan Mo; Jennifer A Pacheco; Jie Xu; Enid Montague; William K Thompson; Joshua C Denny; Christopher G Chute; Jyotishman Pathak
Journal:  J Biomed Inform       Date:  2016-07-05       Impact factor: 6.317

Review 3.  QSAR without borders.

Authors:  Eugene N Muratov; Jürgen Bajorath; Robert P Sheridan; Igor V Tetko; Dmitry Filimonov; Vladimir Poroikov; Tudor I Oprea; Igor I Baskin; Alexandre Varnek; Adrian Roitberg; Olexandr Isayev; Stefano Curtarolo; Denis Fourches; Yoram Cohen; Alan Aspuru-Guzik; David A Winkler; Dimitris Agrafiotis; Artem Cherkasov; Alexander Tropsha
Journal:  Chem Soc Rev       Date:  2020-05-01       Impact factor: 54.564

4.  Improving data and knowledge management to better integrate health care and research.

Authors:  M Cases; L I Furlong; J Albanell; R B Altman; R Bellazzi; S Boyer; A Brand; A J Brookes; S Brunak; T W Clark; J Gea; P Ghazal; N Graf; R Guigó; T E Klein; N López-Bigas; V Maojo; B Mons; M Musen; J L Oliveira; A Rowe; P Ruch; A Shabo; E H Shortliffe; A Valencia; J van der Lei; M A Mayer; F Sanz
Journal:  J Intern Med       Date:  2013-07-15       Impact factor: 8.989

5.  Resolving complex research data management issues in biomedical laboratories: Qualitative study of an industry-academia collaboration.

Authors:  Sahiti Myneni; Vimla L Patel; G Steven Bova; Jian Wang; Christopher F Ackerman; Cynthia A Berlinicke; Steve H Chen; Mikael Lindvall; Donald J Zack
Journal:  Comput Methods Programs Biomed       Date:  2015-11-12       Impact factor: 5.428

Review 6.  Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling.

Authors:  Linlin Zhao; Heather L Ciallella; Lauren M Aleksunes; Hao Zhu
Journal:  Drug Discov Today       Date:  2020-07-11       Impact factor: 7.851

Review 7.  Reuse of public genome-wide gene expression data.

Authors:  Johan Rung; Alvis Brazma
Journal:  Nat Rev Genet       Date:  2012-12-27       Impact factor: 53.242

8.  Marine bacteria exhibit a bipolar distribution.

Authors:  Woo Jun Sul; Thomas A Oliver; Hugh W Ducklow; Linda A Amaral-Zettler; Mitchell L Sogin
Journal:  Proc Natl Acad Sci U S A       Date:  2013-01-16       Impact factor: 11.205

Review 9.  Text-mining solutions for biomedical research: enabling integrative biology.

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Journal:  Nat Rev Genet       Date:  2012-11-14       Impact factor: 53.242

Review 10.  Transcriptomics and proteomics in stem cell research.

Authors:  Hai Wang; Qian Zhang; Xiangdong Fang
Journal:  Front Med       Date:  2014-06-27       Impact factor: 4.592

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