publication . Article . 2015

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Jun Zhao;
  • Published: 01 Jan 2015
Abstract
Motivation Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assesse...
Subjects
free text keywords: Research Article, Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Ontology (information science), Scripting language, computer.software_genre, computer, Natural language, Data modeling, Workflow, Data processing, Physics, Bioinformatics, Executable, computer.file_format, Publication, business.industry, business
Related Organizations
Funded by
EC| RD-CONNECT
Project
RD-CONNECT
RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research
  • Funder: European Commission (EC)
  • Project Code: 305444
  • Funding stream: FP7 | SP1 | HEALTH
,
EC| OPEN PHACTS
Project
OPEN PHACTS
The Open Pharmacological Concepts Triple Store
  • Funder: European Commission (EC)
  • Project Code: 115191
  • Funding stream: FP7 | SP1 | SP1-JTI
,
RCUK| COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024101/1
  • Funding stream: BBSRC
,
RCUK| Building a global metagenomics portal ('MGportal') to handle next-generation sequencing data and associated metadata
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/I025840/1
  • Funding stream: BBSRC
86 references, page 1 of 6

1 Naik G. Scientists’ Elusive Goal: Reproducing Study Results. Wall Street Journal. 2011; Available from: http://online.wsj.com/news/articles/SB10001424052970203764804577059841672541590 [cited 15 October 2013].

2 Casadevall A, Fang FC. Reproducible science. Infection and immunity. 2010 Dec;78(12):4972–4975. Available from: 10.1128/IAI.00908-10 [OpenAIRE] [DOI]

3 Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 3;483(7391):531–533. Available from: 10.1038/483531a 22460880 [OpenAIRE] [PubMed] [DOI]

4 Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, et al Repeatability of published microarray gene expression analyses. Nature Genetics. 2009 2;41(2):149–155. Available from: 10.1038/ng.295 19174838 [OpenAIRE] [PubMed] [DOI]

5 Cokol M, Ozbay F, Rodriguez-Esteban R. Retraction rates are on the rise. EMBO Rep. 2008 1;9(1):2 Available from: 10.1038/sj.embor.7401143 18174889 [OpenAIRE] [PubMed] [DOI]

6 GigaScience Journal;. Available from: http://www.gigasciencejournal.com/

7 Scientific Data;. Available from: http://www.nature.com/sdata/

8 OECD Principles and Guidelines for Access to Research Data from Public Funding;. Available from: http://www.oecd.org/sti/sci-tech/38500813.pdf

9 Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities;. Available from: http://openaccess.mpg.de/

10 Royal Society—Science as an open enterprise;. Available from: https://royalsociety.org/~/media/Royal_Society_Content/policy/projects/sape/2012-06-20-SAOE.pdf

11 Research Data Alliance;. Available from: https://rd-alliance.org/

12 The Future of Research Communications and e-Scholarship (Force11);. Available from: https://www.force11.org/white_paper

13 National Institutes of Health - Plan for Increasing Access to Scientific Publications and Digital Scientific Data from NIH Funded Scientific Research;. Available from: http://grants.nih.gov/grants/NIH-Public-Access-Plan.pdf

14 Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, et al Toward interoperable bioscience data. Nature Genetics. 2012 2;44(2):121–126. Available from: 10.1038/ng.1054 22281772 [OpenAIRE] [PubMed] [DOI]

15 Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, et al Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004;20(17):3045–3054. Available from: 10.1093/bioinformatics/bth361 15201187 [OpenAIRE] [PubMed] [DOI]

86 references, page 1 of 6
Abstract
Motivation Reproducing the results from a scientific paper can be challenging due to the absence of data and the computational tools required for their analysis. In addition, details relating to the procedures used to obtain the published results can be difficult to discern due to the use of natural language when reporting how experiments have been performed. The Investigation/Study/Assay (ISA), Nanopublications (NP), and Research Objects (RO) models are conceptual data modelling frameworks that can structure such information from scientific papers. Computational workflow platforms can also be used to reproduce analyses of data in a principled manner. We assesse...
Subjects
free text keywords: Research Article, Medicine, R, Science, Q, General Biochemistry, Genetics and Molecular Biology, General Agricultural and Biological Sciences, General Medicine, Ontology (information science), Scripting language, computer.software_genre, computer, Natural language, Data modeling, Workflow, Data processing, Physics, Bioinformatics, Executable, computer.file_format, Publication, business.industry, business
Related Organizations
Funded by
EC| RD-CONNECT
Project
RD-CONNECT
RD-CONNECT: An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research
  • Funder: European Commission (EC)
  • Project Code: 305444
  • Funding stream: FP7 | SP1 | HEALTH
,
EC| OPEN PHACTS
Project
OPEN PHACTS
The Open Pharmacological Concepts Triple Store
  • Funder: European Commission (EC)
  • Project Code: 115191
  • Funding stream: FP7 | SP1 | SP1-JTI
,
RCUK| COpenPlantOmics (COPO): a Collaborative Bioinformatics Plant Science Platform
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/L024101/1
  • Funding stream: BBSRC
,
RCUK| Building a global metagenomics portal ('MGportal') to handle next-generation sequencing data and associated metadata
Project
  • Funder: Research Council UK (RCUK)
  • Project Code: BB/I025840/1
  • Funding stream: BBSRC
86 references, page 1 of 6

1 Naik G. Scientists’ Elusive Goal: Reproducing Study Results. Wall Street Journal. 2011; Available from: http://online.wsj.com/news/articles/SB10001424052970203764804577059841672541590 [cited 15 October 2013].

2 Casadevall A, Fang FC. Reproducible science. Infection and immunity. 2010 Dec;78(12):4972–4975. Available from: 10.1128/IAI.00908-10 [OpenAIRE] [DOI]

3 Begley CG, Ellis LM. Drug development: Raise standards for preclinical cancer research. Nature. 2012 3;483(7391):531–533. Available from: 10.1038/483531a 22460880 [OpenAIRE] [PubMed] [DOI]

4 Ioannidis JP, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC, et al Repeatability of published microarray gene expression analyses. Nature Genetics. 2009 2;41(2):149–155. Available from: 10.1038/ng.295 19174838 [OpenAIRE] [PubMed] [DOI]

5 Cokol M, Ozbay F, Rodriguez-Esteban R. Retraction rates are on the rise. EMBO Rep. 2008 1;9(1):2 Available from: 10.1038/sj.embor.7401143 18174889 [OpenAIRE] [PubMed] [DOI]

6 GigaScience Journal;. Available from: http://www.gigasciencejournal.com/

7 Scientific Data;. Available from: http://www.nature.com/sdata/

8 OECD Principles and Guidelines for Access to Research Data from Public Funding;. Available from: http://www.oecd.org/sti/sci-tech/38500813.pdf

9 Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities;. Available from: http://openaccess.mpg.de/

10 Royal Society—Science as an open enterprise;. Available from: https://royalsociety.org/~/media/Royal_Society_Content/policy/projects/sape/2012-06-20-SAOE.pdf

11 Research Data Alliance;. Available from: https://rd-alliance.org/

12 The Future of Research Communications and e-Scholarship (Force11);. Available from: https://www.force11.org/white_paper

13 National Institutes of Health - Plan for Increasing Access to Scientific Publications and Digital Scientific Data from NIH Funded Scientific Research;. Available from: http://grants.nih.gov/grants/NIH-Public-Access-Plan.pdf

14 Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, et al Toward interoperable bioscience data. Nature Genetics. 2012 2;44(2):121–126. Available from: 10.1038/ng.1054 22281772 [OpenAIRE] [PubMed] [DOI]

15 Oinn T, Addis M, Ferris J, Marvin D, Senger M, Greenwood M, et al Taverna: a tool for the composition and enactment of bioinformatics workflows. Bioinformatics. 2004;20(17):3045–3054. Available from: 10.1093/bioinformatics/bth361 15201187 [OpenAIRE] [PubMed] [DOI]

86 references, page 1 of 6
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publication . Article . 2015

From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics

Jun Zhao;