ArticlePloS one2015
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Assessing computational reproducibility in Behavior Research Methods.Behavior research methods · 2024Article
- Scientific modelling can be accessible, interoperable and user friendly: A case study for pasture and livestock modelling in Spain.PloS one · 2023Article
- Recommendations for Reporting Machine Learning Analyses in Clinical Research.Circulation. Cardiovascular quality and outcomes · 2020Article
- Looking back: forward looking.GigaScience · 2017Article
- repo: an R package for data-centered management of bioinformatic pipelines.BMC bioinformatics · 2017Article
- AVOCADO: Visualization of Workflow-Derived Data Provenance for Reproducible Biomedical Research.Computer graphics forum : journal of the European Association for Computer Graphics · 2016Article
- The FAIR Guiding Principles for scientific data management and stewardship.Scientific data · 2016Article
- Better reporting for better research: a checklist for reproducibility.Genome biology · 2015Article
- Better reporting for better research: a checklist for reproducibility.BMC neuroscience · 2015Article
- Introduction to the Rosetta Special Collection.PloS one · 2015Article
- Better reporting for better research: a checklist for reproducibility.GigaScience · 2015Article
- Erratum: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler.GigaScience · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors.
Funding
Abstract
motivationReproducing 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.
resultsExecutable 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.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.