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Year of Publication
1.  GigaDB: promoting data dissemination and reproducibility 
Often papers are published where the underlying data supporting the research are not made available because of the limitations of making such large data sets publicly and permanently accessible. Even if the raw data are deposited in public archives, the essential analysis intermediaries, scripts or software are frequently not made available, meaning the science is not reproducible. The GigaScience journal is attempting to address this issue with the associated data storage and dissemination portal, the GigaScience database (GigaDB). Here we present the current version of GigaDB and reveal plans for the next generation of improvements. However, most importantly, we are soliciting responses from you, the users, to ensure that future developments are focused on the data storage and dissemination issues that still need resolving.
Database URL: http://www.gigadb.org
doi:10.1093/database/bau018
PMCID: PMC3950661  PMID: 24622612
2.  Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data 
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
doi:10.3897/BDJ.1.e1013
PMCID: PMC3964625  PMID: 24723752
Cybertaxonomy; gene sequence data; micro-CT; data integration; molecular systematics; caves; Croatia; biospeleology
3.  Biodiversity research in the “big data” era: GigaScience and Pensoft work together to publish the most data-rich species description 
GigaScience  2013;2:14.
With the publication of the first eukaryotic species description, combining transcriptomic, DNA barcoding, and micro-CT imaging data, GigaScience and Pensoft demonstrate how classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. This 'holistic’ approach in taxonomic description of a new species of cave-dwelling centipede is published in the Biodiversity Data Journal (BDJ), with coordinated data release in the GigaScience GigaDB database.
doi:10.1186/2047-217X-2-14
PMCID: PMC4076509  PMID: 24229463
4.  Eastern genomics promises 
Genome Biology  2012;13(7):317.
A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
doi:10.1186/gb-2012-13-7-317
PMCID: PMC3491378  PMID: 22805712
5.  Peering into peer-review at GigaScience 
GigaScience  2013;2:1.
Fostering and promoting more open and transparent science is one of the goals of GigaScience. One of the ways we have been doing this is by throwing light on the peer-review process and carrying out open peer-review as standard. In this editorial, we provide our rationale for undertaking this policy, give examples of our positive experiences to date, and encourage others to open up the normally opaque publication process.
doi:10.1186/2047-217X-2-1
PMCID: PMC3626537  PMID: 23587291
6.  Toward interoperable bioscience data 
Nature genetics  2012;44(2):121-126.
To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open ‘data commoning’ culture. Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared ‘Investigation-Study-Assay’ framework to support that vision.
doi:10.1038/ng.1054
PMCID: PMC3428019  PMID: 22281772
7.  Large and linked in scientific publishing 
GigaScience  2012;1:1.
We are delighted to announce the launch of GigaScience, an online open-access journal that focuses on research using or producing large datasets in all areas of biological and biomedical sciences. GigaScience is a new type of journal that provides standard scientific publishing linked directly to a database that hosts all the relevant data. The primary goals for the journal, detailed in this editorial, are to promote more rapid data release, broader use and reuse of data, improved reproducibility of results, and direct, easy access between analyses and their data. Direct and permanent connections of scientific analyses and their data (achieved by assigning all hosted data a citable DOI) will enable better analysis and deeper interpretation of the data in the future.
doi:10.1186/2047-217X-1-1
PMCID: PMC3617448  PMID: 23587310
8.  GigaDB: announcing the GigaScience database 
GigaScience  2012;1:11.
With the launch of GigaScience journal, here we provide insight into the accompanying database GigaDB, which allows the integration of manuscript publication with supporting data and tools. Reinforcing and upholding GigaScience’s goals to promote open-data and reproducibility of research, GigaDB also aims to provide a home, when a suitable public repository does not exist, for the supporting data or tools featured in the journal and beyond.
doi:10.1186/2047-217X-1-11
PMCID: PMC3626507  PMID: 23587345
9.  Adventures in data citation: sorghum genome data exemplifies the new gold standard 
BMC Research Notes  2012;5:223.
Scientific progress is driven by the availability of information, which makes it essential that data be broadly, easily and rapidly accessible to researchers in every field. In addition to being good scientific practice, provision of supporting data in a convenient way increases experimental transparency and improves research efficiency by reducing unnecessary duplication of experiments. There are, however, serious constraints that limit extensive data dissemination. One such constraint is that, despite providing a major foundation of data to the advantage of entire community, data producers rarely receive the credit they deserve for the substantial amount of time and effort they spend creating these resources. In this regard, a formal system that provides recognition for data producers would serve to incentivize them to share more of their data.
The process of data citation, in which the data themselves are cited and referenced in journal articles as persistently identifiable bibliographic entities, is a potential way to properly acknowledge data output. The recent publication of several sorghum genomes in Genome Biology is a notable first example of good data citation practice in the field of genomics and demonstrates the practicalities and formatting required for doing so. It also illustrates how effective use of persistent identifiers can augment the submission of data to the current standard scientific repositories.
doi:10.1186/1756-0500-5-223
PMCID: PMC3392744  PMID: 22571506
10.  Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012. 
Standards in Genomic Sciences  2012;6(2):276-286.
This report details the outcome of the 13th Meeting of the Genomic Standards Consortium. The three-day conference was held at the Kingkey Palace Hotel, Shenzhen, China, on March 5–7, 2012, and was hosted by the Beijing Genomics Institute. The meeting, titled From Genomes to Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample. To this end the meeting focused on genomic projects for animals, plants, fungi, and viruses; metagenomic studies in host-microbe interactions; and the dynamics of microbial communities. In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored by the Alfred P. Sloan Foundation.
doi:10.4056/sigs.2876184
PMCID: PMC3387801  PMID: 22768370
Genomic Standards Consortium; microbiome; microbial metagenomics; fungal genomics; viral genomics; Genomic Observatories Network
11.  BMC Biology turns five 
BMC Biology  2008;6:53.
doi:10.1186/1741-7007-6-53
PMCID: PMC2625334  PMID: 19087238

Results 1-11 (11)