From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
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...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4495984?pdf=render |
| _version_ | 1811322912457621504 |
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| author | Alejandra González-Beltrán Peter Li Jun Zhao Maria Susana Avila-Garcia Marco Roos Mark Thompson Eelke van der Horst Rajaram Kaliyaperumal Ruibang Luo Tin-Lap Lee Tak-Wah Lam Scott C Edmunds Susanna-Assunta Sansone Philippe Rocca-Serra |
| author_facet | Alejandra González-Beltrán Peter Li Jun Zhao Maria Susana Avila-Garcia Marco Roos Mark Thompson Eelke van der Horst Rajaram Kaliyaperumal Ruibang Luo Tin-Lap Lee Tak-Wah Lam Scott C Edmunds Susanna-Assunta Sansone Philippe Rocca-Serra |
| author_sort | Alejandra González-Beltrán |
| collection | DOAJ |
| description | 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 assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler. RESULTS:Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. AVAILABILITY:SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/. CONTACT:philippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk. |
| first_indexed | 2024-04-13T13:44:39Z |
| format | Article |
| id | doaj.art-5bbb66e760e14190a36de621fdf2c61c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T13:44:39Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-5bbb66e760e14190a36de621fdf2c61c2022-12-22T02:44:31ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-01107e012761210.1371/journal.pone.0127612From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.Alejandra González-BeltránPeter LiJun ZhaoMaria Susana Avila-GarciaMarco RoosMark ThompsonEelke van der HorstRajaram KaliyaperumalRuibang LuoTin-Lap LeeTak-Wah LamScott C EdmundsSusanna-Assunta SansonePhilippe Rocca-SerraMOTIVATION: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 assessed the extent by which ISA, NP, and RO models, together with the Galaxy workflow system, can capture the experimental processes and reproduce the findings of a previously published paper reporting on the development of SOAPdenovo2, a de novo genome assembler. RESULTS:Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published findings. A structured representation of the information in the SOAPdenovo2 paper was produced by combining the use of ISA, NP, and RO models. By structuring the information in the published paper using these data and scientific workflow modelling frameworks, it was possible to explicitly declare elements of experimental design, variables, and findings. The models served as guides in the curation of scientific information and this led to the identification of inconsistencies in the original published paper, thereby allowing its authors to publish corrections in the form of an errata. AVAILABILITY:SOAPdenovo2 scripts, data, and results are available through the GigaScience Database: http://dx.doi.org/10.5524/100044; the workflows are available from GigaGalaxy: http://galaxy.cbiit.cuhk.edu.hk; and the representations using the ISA, NP, and RO models are available through the SOAPdenovo2 case study website http://isa-tools.github.io/soapdenovo2/. CONTACT:philippe.rocca-serra@oerc.ox.ac.uk and susanna-assunta.sansone@oerc.ox.ac.uk.http://europepmc.org/articles/PMC4495984?pdf=render |
| spellingShingle | Alejandra González-Beltrán Peter Li Jun Zhao Maria Susana Avila-Garcia Marco Roos Mark Thompson Eelke van der Horst Rajaram Kaliyaperumal Ruibang Luo Tin-Lap Lee Tak-Wah Lam Scott C Edmunds Susanna-Assunta Sansone Philippe Rocca-Serra From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PLoS ONE |
| title | From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. |
| title_full | From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. |
| title_fullStr | From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. |
| title_full_unstemmed | From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. |
| title_short | From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. |
| title_sort | from peer reviewed to peer reproduced in scholarly publishing the complementary roles of data models and workflows in bioinformatics |
| url | http://europepmc.org/articles/PMC4495984?pdf=render |
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