Journal ID (nlm-ta): PLoS One
Journal ID (iso-abbrev): PLoS ONE
Journal ID (publisher-id): plos
Journal ID (pmc): plosone
Title:
PLoS ONE
Publisher:
Public Library of Science
(San Francisco, CA USA
)
ISSN
(Electronic):
1932-6203
Publication date Collection: 2015
Publication date
(Electronic):
8
July
2015
Volume: 10
Issue: 7
Electronic Location Identifier: e0127612
Affiliations
[1
]Oxford e-Research Centre, University of Oxford, 7 Keble Road, OX1 3QG, United Kingdom
[2
]GigaScience, BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate,
Hong Kong, People’s Republic of China
[3
]InfoLab21, Lancaster University, Bailrigg, Lancaster, LA1 4WA, United Kingdom
[4
]Nuffield Department of Medicine, Experimental Medicine Division, John Radcliffe Hospital,
Headley Way, Headington, Oxford, OX3 9DU, United Kingdom
[5
]Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300
RC Leiden, The Netherlands
[6
]HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department
of Computer Science, University of Hong Kong, Pokfulam, Hong Kong, People’s Republic
of China
[7
]School of Biomedical Sciences and CUHK-BGI Innovation Institute of Trans-omics, The
Chinese University of Hong Kong, Shatin, Hong Kong, People’s Republic of China
University of Illinois-Chicago, UNITED STATES
Author notes
Competing Interests: The authors have declared that no competing interests exist.
Conceived and designed the experiments: SAS AGB PRS JZ MR. Performed the experiments:
AGB PRS PL. Analyzed the data: AGB PRS PL. Contributed reagents/materials/analysis
tools: RL TWL TLL PL. Wrote the paper: PRS AGB SAS PL JZ MR SCE MSAG. Proposed the
idea after an initial meeting with JZ, MR, AGB, and PRS: SAS. Selected the publication
and worked with its authors (RL, TWL): SCE PL. Did ISA-Tab, linkedISA RDF, NPs representation
and SPARQL queries over linkedISA and NPs: PRS AGB. Reviewed the NPs: MR MT. Submitted
terms to OBI: PRS. Wrote linkedISA, NanoMaton software and prepared dedicated website
and triple store: AGB. Re-implemented the published SOAPdenovo2 analyses as Galaxy
workflows with help from SCE, RL, and TWL: PL TLL. Created the Research Object with
input from MSAG and PRS: JZ. Wrote the manuscript first draft: PRS. Contributed to
the final version, read it, and approved it: PRS AGB PL JZ MSAG MR MT EH RK RL TLL
TWL SCE SAS. Contributed to the review of the nanopublications produced by PRS and
AGB: EH RK.
Article
Publisher ID:
PONE-D-14-54465
DOI: 10.1371/journal.pone.0127612
PMC ID: 4495984
PubMed ID: 26154165
SO-VID: f688505d-7fd5-4eff-a37c-2cec4455273c
Copyright statement:
Copyright @
2015
License:
This is an open access article distributed under the terms of the
Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided
the original author and source are credited
SAS, PRS, and AGB received funding from the European Union Coordination of Standards
in Metabolomics (COSMOS) FP7 E9RXDC00, the British Biotechnology and Biological Science
Research Council BB/L024101/1, BB/I025840/1, and the University of Oxford e-Research
Centre. The work done by PL, SCE, and TLL on GigaGalaxy and the implementation of
the SOAPdenovo2 workflows were supported by funding from the joint Chinese University
of Hong Kong (CUHK)/The Beijing Genome Institute (BGI) Innovation Institute of Trans-omics
and School of Biomedical Sciences, The Chinese University of Hong Kong (CUHK) and
the China National GeneBank (CNGB). MSAG and JZ are supported by the European Union
Workflow4ever project (EU Wf4Ever STREP, 270129), funded under European Union Framework
Program 7 (EU-FP7 ICT-2009.4.1). MR, MT, EH, and RK are supported by the European
Union Workflow4ever project (EU Wf4Ever STREP, 270129) funded under European Union
Framework Program 7 (EU-FP7 ICT-2009.4.1), the Innovative Medicines Initiative Joint
Undertaking (IMI-JU) project Open PHACTS (grant agreement no. 115191), and the European
Union RD-Connect (EU FP7/2007-2013, grant agreement no. 305,444). SOAPdenovo2 was
developed with the support of the State Key Development Program for Basic Research
of China-973 Program (2011CB809203); National High Technology Research and Development
Program of China-863 program (2012AA02A201); the National Natural Science Foundation
of China (90612019); the Shenzhen Key Laboratory of Trans-omics Biotechnologies (CXB201108250096A);
and the Shenzhen Municipal Government of China (JC201005260191A and CXB201108250096A).
Tak-Wah Lam was partially supported by RGC General Research Fund 10612042.