FAIRer knowledge about biodiversity with AI-friendly nanopublications at Biodiversity Data Journal

Earlier this year, in a pilot project, the teams of high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft released a novel workflow to publicly share and future-proof scientific findings by means of nanopublications.

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability. By making it easier to trace individual findings back to their origin and/or follow-up updates, it also helps to better understand the provenance of biodiversity data.

These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.

Now, the collaborators – also partly supported by the Horizon 2020-funded project BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library) – have built up on a pilot workflow already launched in the Biodiversity Data Journal – to create a specialised nanopublication solution to address the need for FAIR (Findable, Accessible, Interoperable and Reusable) data in the biodiversity science domain. 

In their studies, researchers need to use and refer to extensive and diverse biodiversity data at once, e.g. information about groups of organisms and their classification, collections, authors and genetic sequences. However, those would normally be scattered across a vast number of articles or belong to dissociated databases. This is a major and widely recognised issue in biodiversity science, which is currently stagnating progress not only in building up the world’s knowledge about the natural world around us, but also impeding biodiversity conservation and ecosystem restoration.

Using the newly released nanopublication workflow, biodiversity researchers can now incorporate nanopublications within their manuscripts to future-proof their most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments. 

In addition, the authors can also create standalone nanopublications that comment or derive from already existing research journals published in an academic journal or another citable source (e.g. expert database), regardless of the author of the source. 

“With the nanopublication format, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in a machine-actionable and FAIR manner. Thus, their contributions to science become future-proof for a reality driven by AI technology,”

explains Prof. Lyubomir Penev, founder and CEO at Pensoft.

“Biodiversity is the ideal field for this pilot exploring the next steps in scientific publishing. Biodiversity and its neighbouring fields have produced a remarkable number of high-quality resources, such as controlled vocabularies and databases, which we can now build upon. Moreover, many Biodiversity researchers have shown to be very open to such new methods and are enthusiastic about working together to build a more powerful ecosystem for scientific knowledge sharing, and we share their enthusiasm,”

says Tobias Kuhn, CTO and co-founder of Knowledge Pixels. 

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You can find more about the nanopublication workflow and its advantages to biodiversity scientists on the Pensoft blog and the Biodiversity Data Journal website.

Biodiversity Data Journal in Science Citation Index Expanded & Journal Citation Reports

Nearly five years after the launch of the innovative, open access scholarly venue, designed to accelerate biodiversity research by closing the gap between narrative and machine-readable structured data, BDJ is formally recognised as one of the high quality journals in its discipline by Clarivate Analytics.

Following a rigorous evaluation process, Pensoft‘s Biodiversity Data Journal (BDJ) was accepted for a range of Clarivate Analytics products and services, including the Science Citation Index Expanded (SCIE) and the Journal Citation Reports, meaning it is to make use of the Journal Impact Factor and related metrics.

Furthermore, articles published in BDJ are to be abstracted in several databases: Agriculture, Biology, and Environmental SciencesZoological RecordBiological Abstracts and BIOSIS Previews, so that the publications are even easier to find by researchers, while citations are continuously tracked, assessed and analysed.

Unlike conventional scholarly journals, BDJ allows for the integrated publication of data alongside text, made possible through highly automated import and conversion of machine-readable structured data into human-accessible format, resulting in a wide range of article types: data papers, species occurrences, species conservation profiles, software descriptions and others. On the other hand, text published in BDJ can be easily downloaded as data or mined by computers for reuse.

“Going beyond the purposes and capabilities of a traditional scholarly journal, or even a data journal, for five years now, BDJ has been successfully demonstrating how much of a valuable scholarly outlet it really is, especially when it comes to publication of data meant to be optimally findable, accessible, interoperable and reusable to the benefit of the field of biodiversity research,” says Prof. Lyubomir Penev, CEO and founder of both Biodiversity Data Journal and Pensoft.

“This recognition from Clarivate is certainly a great reassurance that BDJ has managed to fulfill its mission in proving its worth on the scholarly scene. After all, it comes with the leading usage metrics, in addition to the already featured AltmetricsDimensionsScopus, and article- and sub-article-level statistics,” he adds.

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About Biodiversity Data Journal:

Biodiversity Data Journal (BDJ) is a community peer-reviewed, open access journal, designed to accelerate publishing, dissemination and sharing of biodiversity-related data of any kind. All structural elements of the articles – text, morphological descriptions, occurrences, data tables, etc. – are treated and stored as data. BDJ aims at integrating data and narrative in the article content to the maximum extent possible. Supplementary data files that underpin graphs, hypotheses and results should also be published with the article or deposited in trusted open access data repositories. The journal provides rich biodiversity data import and export facilities through the ARPHA Writing Tool and Darwin Core Archives.

Research Ideas & Outcomes: New open-access journal to publish entire research cycles

Research Ideas & Outcomes (RIO), a new open access journal, is formally announced. The new journal represents a paradigm shift in academic publishing: for the first time, RIO will publish research from all stages of the research cycle, across a broad suite of disciplines, from humanities to science.

Traditional journals accept only articles produced at the end of the research continuum, long after the core work has been completed. RIO will publish ideas and outputs from all stages of the research cycle: proposals, experimental designs, data, software, research articles, project reports, policy briefs, project management plans and more.

The journal takes another step ahead with a collaborative platform that allows all ideas and outputs to be labelled with Impact Categories based upon UN Millennium Development Goals(MDGs) and EU Societal Challenges. These categories provide social impact-based labelling to help funders, journalists and the wider public discover and finance relevant research as well as to foster interdisciplinary collaboration around societal challenges.

These game-changing ideas come packed with technical innovation and unique features. The journal is published through ARPHA, the first publishing platform ever to support the full life cycle of a manuscript: from authoring to submission, public peer review, publication and dissemination, within a single, fully-integrated online collaborative environment. The new platform will also allow for RIO to offer one of the most transparent, open and public peer review processes, thus building trust in the reviewed outcomes.

These features come à la carte: RIO will offer flexible pricing where authors can choose exactly which publishing services fit their needs and budget. All its contents – including reviews and comments, data and code – will receive a persistent unique identifier, will be permanently archived and made available under open licenses without any access embargo.

“RIO is not just about different kinds of submissions, though that is a crucial feature and certainly unique for publishing ongoing or even proposed research: it is also about linking those submissions together across the research cycle, about reducing the time from submission to publication, about collaborative authoring and reviewing, about mapping to societal challenges, about technical innovation, about enabling reuse and about giving authors more choice in what features they actually want from the journal.” said Dr. Daniel Mietchen, a founding editor of RIO.

I’m proud to pioneer the first journal which can publish research from all stages of the research process,” said Prof. Lyubomir Penev, Co-Founder of RIO and Pensoft. “For the first time, researchers can get formal publication credit for previously ‘hidden’ parts of their work like written research proposals. We can publish all outputs in one journal; the same journal – RIO.

RIO is scheduled to start accepting manuscripts in November 2015.