Corresponding author: Vincent Smith (
Academic editor: Lyubomir Penev
Driven by changes to policies of governments and funding agencies, Open Access to content and data is quickly becoming the prevailing model in academic publishing. Open Access benefits scientists with greater dissemination and citation of their work, and provides society as a whole with access to the latest research. Open Access is, however, only one facet of scholarly communication. Core scientific statements or assertions are intertwined and hidden in the scholarly narratives, and the data underlying these statements are often obscured to the point that replication of results is impossible (
An often cited reason for the lack of published data is the absence of a reward mechanism for the individuals involved in creating and managing information (
If we are going to incentivise the mass publication of data, we also need mechanisms to ensure quality. Traditional peer review is one of the bottlenecks in standard publication practice (
An abundance of small isolated datasets does not, however, allow us to address the fundamental problems within the biodiversity science community. These islands of data are only of value if connected and interlinked. The task of interlinking is performed by biodiversity data aggregators like the
Works of potentially very limited length can hold intrinsic value to the community, but are almost impossible to publish in traditional journals chasing impact factors. Examples include single species descriptions, local checklists and software descriptions, or ecological surveys and plot data. An infrastructure that allows datasets of any size to be important means we can publish them at any time. There is no need to wait for datasets to reach a critical mass suitable for publication in a traditional journal.
Today, we are pleased to announce the official release of the first series of papers published in
Most journals nowadays clearly separate data from narrative (text). Moreover, data publishing through data centres and repositories has almost become a separate sector within the scholarly publishing landscape. BDJ is not a conventional journal, nor is it a conventional “data journal”. It aims to integrate data and text in a single publication by converting several kinds of biodiversity data (e.g., species occurrences, checklists, or data tables) into the text for human-readable use, while simultaneously making data units from the same article harvestable and downloadable. The text itself is marked up and presented in a highly structured and machine readable form.
BDJ aims to integrate small data into the text whenever possible. Supplementary data files that underpin graphs, hypotheses and results can also be uploaded on the journal’s website and published with the article.
Nonetheless, this is usually not possible for large or complex data, for which we recommend deposition in an established open international repository (for details, see
Large primary biodiversity data sets (e.g., institutional collections of species-occurrence records) should be published with the Genomic data should be deposited with Phylogenetic data should be deposited at Biodiversity-related geoscience and environmental data should be deposited in Morphological images other than those presented in the article should be deposited at Videos should be uploaded to video sharing sites like Any other large data sets (e.g., ecological observations, environmental data, morphological and other data types) should be deposited in the
All external data used in a BDJ paper must be cited in the reference list, and links to these data (as deposited in external repositories) must be included in a separate data resources section of the article.
All datasets, images or multimedia are freely downloadable from the text under the
By facilitating open access to the data that underlie every publication, BDJ is setting a new standard in transparency and repeatability in biodiversity science. Perpetual and universal access to primary data stimulates scientific progress by helping authors build upon existing datasets. BDJ’s commitment to supporting automated data aggregation and interlinking is happening alongside multiple advances in biodiversity informatics infrastructure that herald the dawning of an era of collaborative, big-data biodiversity science (
The online, collaborative, article-authoring platform (
A special feature of PWT is that the authors can see at any time an editable preview of their manuscript in a format that is very close to the final published version. On completion of the manuscript, it can be submitted to the journal with a simple click of a button that will initiate the review process. The tool also allows automated import of manuscripts from data management platforms such as
A major advantage of the PWT is that it handles much of the semantic enhancement of a manuscript automatically during validation, eliminating the need for the authors or editors to manually markup portions of text. Examples of this include taxonomic names and georeferenced localities. The validation tool checks for compliance with the relevant biological code, for example checking that a holotype designation has been made for a new species description and that a new genus has a designated type species. In the near future, the PWT will also automatically register nomenclatural acts in the appropriate registry (
The technology used by the PWT largely eliminates the conventional layout stage, just as the validation tool saves work for the copyeditors. Our goal is to greatly reduce the publication costs for all. This is particularly important because many authors working within biodiversity science are not backed by large institutions who can cover large page charges.
A novel
There are three groups of reviewers that may participate in the community peer review process:
The editor’s work is reduced by a tool that collates reviewers’ comments and corrections into a single document. Upon receipt of this consolidated review and editorial evaluation (Fig.
Accepted articles are published in semantically enhanced HTML, PDF and XML versions, compliant with the
In the Internet era, dissemination of published information is at least as important as the act of publishing. The highly structured text, domain-specific markup and underlying data can be used not only for effective reading but also to provide users direct access to the precise data they need (
Literature references are exported to the community-owned Bibliography of Life (based on the
Images are exported to
The workflow has been funded in part by the European Union’s Seventh Framework Program (FP7) project
Three-step editorial workflow in the Biodiversity Data Journal: manuscript authoring, peer-review and publication.
Consolidated review version. The editor sees all reviewer's corrections and comments in one place and can filter them out. The editor can also insert his/her own corrections and comments before submitting the editorial evaluation.