Posts tagged: General

Adventures in Data Citation: sorghum as a standard for data release

Scott Edmunds on May 11, 2012 at 10:28 am - 1 Comment

A correspondence we have contributed to has just been published in the BMC Research Notes “Data standardization, sharing and publication series” on the data-citation and data-release practices surrounding the Sorghum genome that is available in our GigaDB database and that was published last year in Genome Biology. We use Sorghum as an example to highlight the issues surrounding data release and use strong words, subtitling the paper “sorghum genome data exemplifies the new gold standard”, justified in this case by the considerable efforts the authors made to go beyond the standards of the field …

What links RNA-Editing, Data Citation and Ancient Chinese Emperors?

Scott Edmunds on February 17, 2012 at 10:05 am - 1 Comment

Another incremental step has been achieved for the adoption of the practice of data citation; this week, Nature Biotechnology has included one of our dataset DOIs in their references for the first time. In "Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome", Zhiyu Peng et al. produced a new pipeline to filter and compare RNA-seq transcriptome and whole genome sequencing data to detect RNA-editing events. Much of the supporting data has been released pre-publication and hosted by our GigaDB database and, as RNA-editing is still quite a controversial

GigaScience Journal Part of Global Data-Sharing Effort: New Standards Allow Disparate Data Sets to Integrate

Scott Edmunds on January 28, 2012 at 2:59 am - 1 Comment

Lead by researchers at the University of Oxford, a group of more than 30 scientific organizations around the globe, have worked to produce a common standard that will make possible the consistent description of enormous and radically different databases compiled in fields ranging from genetics to stem cell science, to environmental studies. One of the contributors playing a role in the project is GigaScience, as we feel it potentially very useful to aid in the handling of the wide-variety of data-types covered by our scope our scope.

The new standard provides a way for scientists in widely disparate fields to co-ordinate each other’s findings by allowing behind-the-scenes combination of …

Data Citation Enters the (year of the) Dragon

Scott Edmunds on January 23, 2012 at 11:15 am - 4 Comments

Today marks the first day of the Chinese Lunar New Year, and as we enter the supposedly auspicious year of the Dragon now is a good opportunity to look towards developments in the nascent field of data publication over the upcoming year. This week marked important announcements of new and improved data publication platforms. Those lucky enough to attend Science Online (or filter through the nearly 30,000 tweets produced by the meetings end!) will have seen the new-look Figshare website promoted in the “Dealing with Data” session, and there has also been good coverage Read more

GigaData news: Macaque DOIs published in Nature Biotechnology

Scott Edmunds on October 21, 2011 at 2:26 am - 3 Comments

This week marks another success for the fledgling practice of data citation, with two datasets from our GigaScience database published in Nature Biotechnology. The genomes sequenced by our colleagues at the BGI for the Cynomolgus and Chinese rhesus macaques were initially released ef=”http://en.wikipedia.org/wiki/Digital_object_identifier” target=”_blank”>DOIs at our launch in July, and were amongst the first (at the time) unpublished genomes released in this way. Data citation is an important concept, allowing data producers to obtain an early form of credit for releasing their work, speeding up research by encouraging early …

GigaScience in the press (and still on the road)…

Scott Edmunds on October 4, 2011 at 7:19 am - 0 Comments

We at GigaScience always appreciate good press, and on top of the welcome coverage on blogs (e.g. this in Annals of Botany) and twitter, we are pleased with the profile of the journal in this months Bio-IT world (especially coming on top of the coverage of our database in the previous issue). The article is a nice introduction to the editors, editorial policies, and hopes for the journal, and is useful reading for those who’d like to know a bit more on top of what …

Papers, papers, papers

Scott Edmunds on August 19, 2011 at 4:42 am - 1 Comment

After last months website launch, and work progressing on our associated GigaScience database (including the addition of further datasets, such as the recently published Chinese Hamster Ovary cell-line genome) our next priority is the more traditional job of an editor: papers, papers papers. The journal has had some great feedback on twitter, on many blogs, and also a nice feature in this months Bio-IT World, so we are now following …

Notes from an E. coli “tweenome” – lessons learned from our first data DOI.

Scott Edmunds on August 3, 2011 at 8:39 am - 7 Comments

Last week marked two important milestones in the deadly 2011 European E. coli 0104:H4 outbreak: the Robert Koch institute announcing the end of the outbreak, and the publication of several papers from the many groups sequencing the pathogen. This included a publication in the New England Journal of Medicine by groups from the BGI, UMC Hamburg-Eppendorf, and Birmingham University acknowledging members of the crowdsourcing community and the work achieved using the genome sequence our colleagues at the BGI made available via our GigaScience database. This was our first dataset released with a Read more

GigaScience, Giga-database and now GigaBlog: new resources for the big-data community

Gabriella Anderson on July 6, 2011 at 5:19 am - 0 Comments

As biological data is now produced faster than it can easily be handled and stored, the dissemination of this data has become a major bottleneck. GigaScience: a new type of journal from BioMed Central and BGI — no stranger to these issues being the world’s largest Genomics center — starts taking submissions today with the goal of addressing many of the issues surrounding “big-data”. Much of the rationale and features of the GigaScience journal and its associated database is presented on our website. But with a scope that covers any biological and biomedical “large-scale” data (and the“(Giga)n” refers to gigantic rather than a specific number), one important question is how exactly are we defining “large-scale”? The …