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From deadly E. coli to endangered polar bears: GigaScience provides first citable data

BioMed Central and BGI launch a new integrated database and journal, to meet the needs of a new generation of biological and biomedical research as it enters the era of "big-data."

GigaScience, an innovative new journal and integrated database to be launched by BioMed Central in November 2011, has released their first datasets to be given a Digital Object Identifier (DOI). This enables a long-needed way to properly recognize the data producers who have provided an untold number of essential resources to the entire research community. This not only promotes very rapid data release, but also provides easy access, reuse, tracking, and most importantly permanency for such datasets. The journal is being launched by a collaboration between BGI, the world's largest genomics institute, and open access publisher BioMed Central, a leader in scientific data sharing and open data.

The datasets, created by BGI and its collaborators in Germany and in the Genome10K project, include the sequence and assembly data from the recent deadly outbreak strain E. coli O104, and 7 large vertebrates, including the giant panda, which is in great danger of extinction; the chinese rhesus and crab-eating cynomolous macaques, which are commonly used biomedical animal models; the polar bear and the emperor and adelie penguins, which live in extremely hostile environments; and the domestic pigeon, which has unusually accurate navigation abilities. The datasets have been assigned Digital Object Identifiers (DOIs) to enable other scientists to cite the datasets, in the same manner as scientific papers.

GigaScience has been working with the DataCite organization and the British Library to enable datasets to be given DOIs. A primary goal for creating dataset DOIs is to promote extremely rapid data release and dissemination. And, in keeping with this, the majority of the above datasets are available prior to the publication of their associated scientific journal articles. Given that such publication is currently the only effective means for data producers to obtain credit for their work, this normally creates extensive delays in data availability due to the long writing, reviewing, and editing processes needed for article publication. This can seriously impede the speed at which scientific discoveries are made.

The importance of free and faster methods of data release was made particularly clear in the recent deadly E. coli outbreak in Europe. To aid the fight against the outbreak, BGI and their collaborators at the University Medical Centre Hamburg-Eppendorf rapidly sequenced the pathogen's genome and immediately released the data. In conjunction with publicizing the rapid release through Twitter, the entire scientific community began to "crowdsource" the data with little to no delay between data production and release. These data were also released without restrictions on its use, under a public domain license. This, in conjunction with having a DOI, marks the first time a genome has been released in this way. Additionally, the growing team of researchers utilizing and adding invaluable information to the pool of data have now confirmed they will also release their work in the same manner.

Speaking of the announcement, Iain Hrynaszkiewicz, Journal Publisher with BioMed Central said: "All the articles published by GigaScience will be freely available for readers and all the data open and reproducible for researchers. An online journal and integrated database enhances the functionality and reliability of the scientific literature and demonstrates real leadership in openness in science. BioMed Central believes open access should include, wherever possible, data as well as papers, and we're delighted to be working with BGI to make data a truly first-class citizen in publishing."


Contact: Matt McKay
BioMed Central

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