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

González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M, Thompson M, van der Horst E, Kaliyaperumal R, Luo R, Lee TL, Lam TW, Edmunds SC, Sansone SA, Rocca-Serra P - PLoS ONE (2015)

Bottom Line: 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.Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published 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.

View Article: PubMed Central - PubMed

Affiliation: Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom.

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 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.

No MeSH data available.


Related in: MedlinePlus

Another view of the complementary aspects of these research object models, highlighting the reliance of persistent identifiers (such as ORCID), and references to Galaxy workflows hosted on GigaScience Servers.
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pone.0127612.g002: Another view of the complementary aspects of these research object models, highlighting the reliance of persistent identifiers (such as ORCID), and references to Galaxy workflows hosted on GigaScience Servers.

Mentions: The nanopublications were created following a novel methodology that combined OntoMaton [42] and NanoMaton [43] software tools. Collected statements were structured as triples in a Google spreadsheet, using the OntoMaton widget, a component of the ISA software suite [42] that accesses community ontologies portals [44, 45]. The collaborative environment allowed review, discussion and incremental improvement until satisfactory expressivity and clarity was reached. The statements were processed with the NanoMaton software component, which converted the OntoMaton templates to RDF. A conceptual overview of how ISA and a nanopublication are related is presented in Fig 1 and Fig 2, while a detailed view, rendered as a graph, is available in Fig 3.


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

González-Beltrán A, Li P, Zhao J, Avila-Garcia MS, Roos M, Thompson M, van der Horst E, Kaliyaperumal R, Luo R, Lee TL, Lam TW, Edmunds SC, Sansone SA, Rocca-Serra P - PLoS ONE (2015)

Another view of the complementary aspects of these research object models, highlighting the reliance of persistent identifiers (such as ORCID), and references to Galaxy workflows hosted on GigaScience Servers.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495984&req=5

pone.0127612.g002: Another view of the complementary aspects of these research object models, highlighting the reliance of persistent identifiers (such as ORCID), and references to Galaxy workflows hosted on GigaScience Servers.
Mentions: The nanopublications were created following a novel methodology that combined OntoMaton [42] and NanoMaton [43] software tools. Collected statements were structured as triples in a Google spreadsheet, using the OntoMaton widget, a component of the ISA software suite [42] that accesses community ontologies portals [44, 45]. The collaborative environment allowed review, discussion and incremental improvement until satisfactory expressivity and clarity was reached. The statements were processed with the NanoMaton software component, which converted the OntoMaton templates to RDF. A conceptual overview of how ISA and a nanopublication are related is presented in Fig 1 and Fig 2, while a detailed view, rendered as a graph, is available in Fig 3.

Bottom Line: 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.Executable workflows were developed using Galaxy, which reproduced results that were consistent with the published 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.

View Article: PubMed Central - PubMed

Affiliation: Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom.

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 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.

No MeSH data available.


Related in: MedlinePlus