From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics.
复制标题
DOI：
10.1371/journal.pone.0127612
复制
发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Rocca-Serra P
中科院分区：
文献类型：
--
作者：
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
由于缺乏数据和分析所需的计算工具，复制科学论文的结果可能具有挑战性。此外，由于在报告如何进行实验时使用自然语言，因此与用于获得已发表结果的程序有关的细节可能难以辨别。调查/研究/分析（伊萨），纳米出版（NP）和研究对象（RO）模型是概念数据建模框架，可以从科学论文中构建此类信息。计算工作流平台也可以用于以有原则的方式再现数据分析。我们评估了伊萨，NP和RO模型与银河工作流系统一起可以捕获实验过程并重现先前发表的关于SOAPDenovo 2（从头基因组组装程序）开发的论文的研究结果的程度。使用银河系统开发了可执行的工作流程，其结果与公布的调查结果一致。通过结合使用伊萨、NP和RO模型，产生了SOAP denovo 2论文中信息的结构化表示。通过使用这些数据和科学工作流程建模框架来构建已发表论文中的信息，可以明确声明实验设计、变量和发现的要素。这些模型在科学信息的管理中起到了指导作用，这导致了对原始发表论文中不一致之处的识别，从而使其作者能够以勘误表的形式发表更正。SOAPDenovo 2脚本、数据和结果可通过GigaScience数据库获得：http：//dx.doi.org/10.5524/100044;工作流可从GigaGalaxy获得：http://galaxy.cbiit.cuhk.edu.hk;使用伊萨、NP和RO模型的表示可通过SOAPDenovo 2案例研究网站http://isa-tools.github.io/soapdenovo2/获得。联系人：philippe. oerc.ox.ac.uk和susanna-assunta. sansone@oerc.ox.ac.uk。
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. 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. 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.
登录
查看更多内容
影响因子：
1.9
作者：
Dumontier M;Baker CJ;Baran J;Callahan A;Chepelev L;Cruz-Toledo J;Del Rio NR;Duck G;Furlong LI;Keath N;Klassen D;McCusker JP;Queralt-Rosinach N;Samwald M;Villanueva-Rosales N;Wilkinson MD;Hoehndorf R
通讯作者：
Hoehndorf R
影响因子：
3.7
作者：
Garijo D;Kinnings S;Xie L;Xie L;Zhang Y;Bourne PE;Gil Y
通讯作者：
Gil Y
影响因子：
1.9
作者：
Brinkman RR;Courtot M;Derom D;Fostel JM;He Y;Lord P;Malone J;Parkinson H;Peters B;Rocca-Serra P;Ruttenberg A;Sansone SA;Soldatova LN;Stoeckert CJ Jr;Turner JA;Zheng J;OBI consortium
通讯作者：
OBI consortium
影响因子：
2.5
作者：
Belhajjame, Khalid;Zhao, Jun;Goble, Carole
通讯作者：
Goble, Carole
DOI：
10.1073/pnas.1017351108
发表时间：
2011-01-25
影响因子：
11.1
作者：
Gnerre, Sante;MacCallum, Iain;Jaffe, David B.
通讯作者：
Jaffe, David B.