1. GigaDB – revolutionizing data dissemination, organization and use
SiZhe Xiao GigaScience 2013
POSTER
Open Access
GigaDB – revolutionizing data dissemination, organization and use
Xiao Si Zhe1 , Chris Hunter, Tam P. Sneddon, Scott C. Edmunds, Alexandra T. Basford, Peter Li, and Laurie Goodman.
Abstract
GigaScience, the online open-access open-data journal, has recently developed GigaDB, a new integrated database of ‘big-data’ studies from the life and biomedical sciences. The initial goals of GigaDB are to assign DOIs to datasets to allow them to be tracked and cited, and to provide a user-friendly web interface to provide easy access to selected GigaDB datasets and files.
We will be working with authors to make the raw data, computational tools and data processing pipelines described in the GigaScience papers available and, where possible, executable on an informatics platform. We hope that by making both the data and processes involved in their analysis freely accessible, this novel form of publication will help articles published in GigaScience to have a much higher impact in the scientific literature, and maximize their reuse within the community.
GigaDB currently accepts submissions in Excel format. Example submission and template files can be found on the website ( To date, GigaDB comprises over 56 datasets and includes Genomic, Transcriptomic, Epigenomic and Metagenomic dataset types but we accept many other dataset types including proteomic and neuroimaging studies.
Future goals include integration with the BGI Cloud, and with the Galaxy software tools to enable users to directly upload files to Galaxy for further analysis. We are also working with ISA-Tab and other scientific standards groups to support and extend the usability and interoperability model.
Keywords: DOI, Galaxy, big-data, database, informatics platform, GigaScience
Background
GigaDB
Growing replication gap:
Home page:
Datasets public in GigaDB
10/18 microarray papers cannot be reproduced
Ioannidis: “Most Published Research Findings Are False”
>15X increase in retracted papers in last decade
Lack of incentives to make data/methods available
Poor metadata quality and lack of interoperability
GigaSolution: deconstructing the paper
Combine and integrate (via citable DOIs):
Open-access journal
Aspera data transfer Faster download speeds
Data Publishing Platform
gigadb.org
GigaDB Submission Workflow
Data Analysis Platform
galaxy.cbiit.cuhk.edu.hk
Curator contacts submitter with DOI citation and to arrange file transfer (and resolve any other questions/issues).
Submitter logs in to GigaDB website and uploads Excel submission
Fail – submitter is provided error report
Linking papers to data and analyses
Curator Review
Excel submission file
Submitter provides files by ftp or Aspera
Open-Paper
Open-Data
Validation checks
DOI assigned
DOI: /100038
Data sets
78GB CC0 data
Files
GigaDB
Linked to
Pass – dataset is uploaded to GigaDB.
DOI
Open-Pipelines
DOI
Open-Workflows
XML is generated and registered with DataCite
Linked to
Analyses
DOI: /100044
Curator makes dataset public (can be set as future date if required)
DataCite XML file
Public GigaDB dataset
DOI /100003
Genomic data from the crab-eating macaque/cynomolgus monkey (Macaca fascicularis) (2011)
Acknowledgements
Thanks to:
Laurie Goodman, Chris Hunter, Scott Edmunds, Tam Sneddon (GigaScience), Shaoguang Liang (BGI-SZ), Qiong Luo, Senghong Wang, Yan Zhou (HKUST), Rob Davidson and Mark Viant (Birmingham Uni), Marco Galardini (Unifi)
doi: /m9.figshare.xxxxx
Cite this poster as: GigaGalaxy: A GigaSolution for reproducible and sustainable genomic data publication and analysis. Scott C. Edmunds, Peter Li, Huayan Gao, Chris Hunter, Si Zhe Zhao, Ruibang Luo, Dennis Chan, Alex Wong, Zhang Yong, Tin-Lap Lee, ISA-TAB team. figshare
Financial support from:
Submit your next manuscript containing large-scale data and workflows to GigaScience and take full advantage of:
Correspondence:
1. BGI HK Research Institute, 16 Dai Fu Street, Tai Po Industrial Estate, Hong Kong SAR, China.
2. BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, China.
3. School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
4. CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
5. HKU-BGI  Bioinformatics Algorithms and Core Tecnology Research Laboratory & Department of Computer Science, University of Hong Kong, Pok Fu Lam, Hong Kong
6. Oxford e-Research Centre, University of Oxford, Oxford, UK.
No space constraints, and unlimited data and workflow hosting in GigaDB and GigaGalaxy
Article processing charges for all submissions in 2013 covered by BGI
Open access, open data and highly visible work freely available for distribution
Inclusion in PubMed and Google Scholar
© 2013 Edmunds et al. This is an Open Access poster distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.