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New GigaDB data resource boosts confidence in unexpected research finding on DNA methylation in nematodes
Today at the Beyond the Genome conference in San Francisco, researchers from BGI were presented with this year’s BioMed Central Open Data Award for their work demonstrating that DNA methylation occurs in the parasitic worm Trichinella spiralis, a human pathogen. Presented by the open access publisher BioMed Central to recognize authors who have demonstrated leadership in the sharing, standardization, publication, or re-use of biomedical research data, this is the 4th time the award has been presented, and the first time to researchers from China. The article, published in Genome Biology, has shaken up the field of epigenetics by shattering the assumption that DNA methylation is absent in nematodes, the tiny worm species that serves as an important model organism for cell and developmental biology research. As a novel and potentially controversial finding, the huge amounts of supporting data were deposited in the journal GigaScience’s database GigaDB to assist others to follow on and reproduce the results.
The judges and editors of Genome Biology were impressed by the numerous extra steps taken by the authors in optimizing the openness and easy accessibility of this data, and were keen to emphasize that the value of open data for such breakthrough science lies not only in providing a resource, but also in conferring transparency to unexpected conclusions that others will naturally wish to challenge. In addition to depositing the raw sequencing and transcriptomic data in the GEO and SRA databases, the authors went beyond standard research practices by making publicly available all additional supporting data in as usable a form as possible and under a CC0 public domain waiver. The authors worked with GigaScience’s GigaDB repository to host associated data types that do not have well-established repositories, and also presented their data in the interoperable ISA-Tab format to maximize its reusability. When asked his thoughts on the value of having the complete set of data available, lead author of the study Dr Fei Gao said, “people will tend to be more confident if they really see the data… They can then test the data by themselves.”
GigaDB is the next generation data repository set up to host data and tools associated with articles in the novel “big-data” journal, GigaScience, and also provides BGI, the world’s largest genomics organization, a way to release their data as rapidly as possible and in a citable format. Partly supported by funding from China National Genebank (CNGB), GigaDB recently relaunched with a new look, and helps meet CNGB and BGI’s aims to provide better support for information sharing and exchange of scientific research. Through an association and associate membership with DataCite consortium, datasets are assigned digital object identifiers to allow them to be independently cited.
In addition to BGI researchers receiving the BMC Open Data Award, BGI has a further presence at the Beyond the Genome meeting with BGI Tech CEO Yingrui Li on the meeting’s organizing committee and researchers presenting talks on BGI’s cutting edge work on prenatal diagnosis and reproductive medicine.
1. Fei Gao, Xiaolei Liu, Xiuping Wu, Xuelin Wang, Desheng Gong, Hanlin Lu, Yudong Xia, Yanxia Song, Junwen Wang, Jing Du, Siyang Liu, Xu Han, Yizhi Tang, Huanming Yang, Qi Jin, Xiuqing Zhang and Mingyuan Liu (2012) Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis. Genome Biology, 13:R100 doi:10.1186/gb-2012-13-10-r100
2. Gao, F; Wang, J; Ji, G (2012): Bisulfite-PCR combined with cloning Sanger sequencing data for validating DNA methylation level in Trichinella spiralis. GigaScience. http://dx.doi.org/10.5524/100043
3. For more on GigaDB see: http://gigadb.org/
4. For more on GigaScience see: http://www.gigasciencejournal.com/