Tag: research

The International Biogeography Society relaunches flagship journal Frontiers of Biogeography on ARPHA platform

“This switch of our journal to a cutting-edge platform, and its committed team of editors, should continue to raise the journal’s visibility and impact,” comments Prof. Dr. Susanne Renner, TIBS President.

The International Biogeography Society (TIBS) has relaunched its flagship open-access scientific journal, Frontiers of Biogeography (FoB), on the ARPHA platform, where it will be co-published with Pensoft Publishers.

This collaboration underscores the society’s commitment to maintaining high-quality, high-visibility and low-cost open-access publishing for the biogeographical community.

“This switch of our journal to a cutting-edge platform, and its committed team of editors, should continue to raise the journal’s visibility and impact,”

comments Prof. Dr. Susanne Renner, TIBS President.

Established by TIBS in 2009, Frontiers of Biogeography serves as an independent forum for research dissemination, and publishes studies on all geographical variations of life at all levels of organisation. The journal adheres to rigorous academic standards, reflecting the mission of TIBS to promote and advance public understanding of biogeographical sciences. 

The journal’s editorial leadership includes Prof. Robert J. Whittaker (University of Oxford, United Kingdom), Dr. Janet Franklin (San Diego State University, USA) and Prof. Mark J. Costello (Nord University, Norway), all esteemed figures in the field.

Frontiers of Biogeography was launched on the ARPHA Platform on the 1st of July 2024. The platform is now open for new submissions and offers a robust review and publication process. Articles and supplementary materials published on ARPHA will be distributed under the Creative Commons Attribution Licence (CC BY 4.0), ensuring wide accessibility and reuse. All previously published issues on the e-Scholarship platform will remain freely accessible, ensuring the continuity of knowledge dissemination.

Frontiers of Biogeography has recently been selected for inclusion in the Web of Science™. Beginning with volume 14(1), articles will be indexed in Emerging Sources Citation Index, Zoological Record, Biological Abstracts, and BIOSIS Previews, significantly enhancing the journal’s visibility.

Furthermore, the journal’s latest Scopus CiteScore of 4.3 places it in the Q1 category for Ecology and Ecology, Evolution, Behaviour and Systematics, and elevates it from Q3 to Q2 in the Global and Planetary Change category.

“I am looking forward to working with the new platform and to the start of a new partnership with our colleagues at Pensoft Publishers. This arrangement underlines the commitment of The International Biogeography Society to the growth and success of Frontiers of Biogeography as a service to our members and the broader scientific community,”

stated Prof. Dr. Robert J. Whittaker, Editor-in-Chief.

“In these days of sometimes exorbitant costs to pay publication charges by some of the big publishers, TIBS and Pensoft are joining forces to make it possible for all authors to be able to publish their work at reasonable costs while maintaining the high scholarly standards of peer-review and editorial management which are the foundation of good science,”

added Prof. Dr. Mark J. Costello, Co-Editor-in-Chief.

“We are excited to welcome Frontiers of Biogeography to the ARPHA Platform and look forward to a successful, open-access future. This partnership aligns with our mission to support scientific research through innovative publishing solutions,”

said Prof. Dr. Lyubomir Penev, CEO and founder of Pensoft Publishers.

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Visit the Frontiers of Biogeography’s new website at https://biogeography.pensoft.net/. Use the Email alert field on the homepage to follow the latest publications, news, and highlights from Frontiers of Biogeography.

You can also follow the journal on X (formerly Twitter) at @newbiogeo.

Keep up to date with the latest from TIBS by following them on X (@Biogeography) and joining the society’s Facebook group.

Vegetation Classification and Survey featured by Web of Science four years after its launch

Vegetation Classification and Survey will soon receive its very first Journal Impact Factor.

Only four years after the inaugural editorial by Prof Dr Florian Jansen, Dr Idoia Biurrun, Prof Dr Jürgen Dengler and Dr Wolfgang Willner that officialised the third and still youngest scientific journal of the International Association of Vegetation Science (IAVS), the Vegetation Classification and Survey (VCS) journal successfully completed the rigorous quality and integrity assessment at Web of Science (WoS).

Late May 2024 saw the whole content ever published in VCS added to the Core Collection of the renowned academic platform, further boosting its discoverability, accessibility and reliability to researchers and other stakeholders alike, confirms the Indexing team of Pensoft and the ARPHA scholarly publishing platform.

“Many thanks to IAVS as owner and Pensoft as publisher, who made this success story possible. However, most of all, this early inclusion into the Web of Science Core Edition is due to the good articles of our authors and the great volunteer service our Associate Editors, Guest Editors, Linguistic Editors, Editorial Review Board members, and other reviewers did and do for VCS,”

the Chief Editors comment on the latest success.

The news means that VCS is soon to receive its very first Journal Impact Factor (JIF): allegedly the most popular and sought after journal-level metric, which annually releases the citation (or “impact”) rate of a given scholarly journal over the last period. By the end of next month, for example, we will know how different journals indexed by WoS have performed compared to each other, based on the number of citations received in 2023 (from other journals indexed by WoS) for papers published in 2021 and 2022 combined.

In 2022, VCS and its all-time publications were also featured by the largest and similarly acclaimed scientific database: Scopus, thus receiving its very first Scopus CiteScore* last June. At 2.0, the result instantly gave a promise of the widely appreciated content published in the journal.

In an editorial, published in the beginning of 2024, the Chief Editors assessed the performance of the journal and analysed the available data from Scopus to predict the citation rates for the journal in the next few years. There, the team also compared the journal’s latest performance with similar journals, including the other two journals owned by the IAVS (i.e. Applied Vegetation Science and Journal of Vegetation Science). Given that as of May 2024 the Scopus CiteScoreTracker for VCS reads 2.5, their optimistic forecasts seem rather realistic.

“The VCS articles of 2023 were on average even better cited than those in Applied Vegetation Science of the same year and had reached about the same level as Journal of Vegetation Science and Biodiversity and Conservation,”

they concluded.

In a recent post, published on the IAVS blog, on behalf of the four VCS Chief Editors, Prof. Dr. Jürgen Dengler further comments on the latest achievements of the journal, while also highlighting particularly valued recent publications.

The team also uses the occasion to invite experts in the field of vegetation science to submit their manuscripts in 2024 to make use of the generous financial support by the IAVS. Given the increasing interest in VCS, the journal also invites additional linguistic editors, as well as reviewers who wish to join the Editorial Review Board.

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Keep yourself updated with news from Vegetation Classification and Survey on X (formerly Twitter) and Facebook. You can also follow IAVS on X and join the Association’s public group on Facebook. 

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*Note that the Scopus database features a different selection of scientific journals compared to Web of Science to estimate citation metrics. The indexers are also using different formulae, where the former looks into citations made in the last two complete years for eligible papers published in the same years.

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About Vegetation Classification and Survey:

Vegetation Classification and Survey (VCS) is an international, peer-reviewed, online journal on plant community ecology published on behalf of the International Association for Vegetation Science (IAVS). It is devoted to vegetation survey and classification at any organisational and spatial scale and without restriction to certain methodological approaches.

The scope of VCS is focused on vegetation typologies and vegetation classification systems, their methodological foundation, their development and their application. The journal publishes original papers that develop new typologies as well as applied studies that use such typologies, for example, in vegetation mapping, ecosystem modelling, nature conservation, land use management, or monitoring. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping, such as algorithms, databases and nomenclatural principles, or are dealing with the conceptual and theoretical bases of vegetation survey and classification. 

VCS also includes two permanent collections (or sections): “Ecoinformatics” and “Phytosociological Nomenclature”. 

About Pensoft:

Pensoft is an independent, open-access publisher and technology provider, best known for its biodiversity journals, including ZooKeys, Biodiversity Data Journal, Phytokeys, Mycokeys, One Ecosystem, Metabarcoding and Metagenomics and many others. To date, the company has continuously been working on various tools and workflows designed to facilitate biodiversity data findability, accessibility, discoverability and interoperability.

About ARPHA Platform:

Pensoft publishes its journals on its self-developed ARPHA publishing platform: an end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. ARPHA provides accomplished and streamlined production workflows that can be heavily customised by client journals not necessarily linked to Pensoft as a publisher, since ARPHA is specially targeted at learned societies, research institutions and university presses. The platform enables a variety of publishing models through a number of options for branding, production and revenue models. Alongside its elaborate and highly automated publishing tools and services, ARPHA provides a range of human-provided services, such as science communication and assistance in indexation at databases like Web of Science and Scopus, to provide a complete full-featured publishing solution package.

How to ensure biodiversity data are FAIR, linked, open and future-proof?

Now concluded Horizon 2020-funded project BiCIKL shares lessons learned with policy-makers and research funders

Within the Biodiversity Community Integrated Knowledge Library (BiCIKL) project, 14 European institutions from ten countries, spent the last three years elaborating on services and high-tech digital tools, in order to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of various types of data about the world’s biodiversity. These types of data include peer-reviewed scientific literature, occurrence records, natural history collections, DNA data and more.

By ensuring all those data are readily available and efficiently interlinked to each other, the project consortium’s intention is to provide better tools to the scientific community, so that it can more rapidly and effectively study, assess, monitor and preserve Earth’s biological diversity in line with the objectives of the likes of the EU Biodiversity Strategy for 2030 and the European Green Deal. Their targets require openly available, precise and harmonised data to underpin the design of effective measures for restoration and conservation, reminds the BiCIKL consortium.

Since 2021, the project partners at BiCIKL have been working together to elaborate existing workflows and links, as well as create brand new ones, so that their data resources, platforms and tools can seamlessly communicate with each other, thereby taking the burden off the shoulders of scientists and letting them focus on their actual mission: paving the way to healthy and sustainable ecosystems across Europe and beyond.

New BiCIKL project to build a freeway between pieces of biodiversity knowledge

Now that the three-year project is officially over, the wider scientific community is yet to reap the fruits of the consortium’s efforts. In fact, the end of the BiCIKL project marks the actual beginning of a European- and global-wide revolution in the way biodiversity scientists access, use and produce data. It is time for the research community, as well as all actors involved in the study of biodiversity and the implementation of regulations necessary to protect and preserve it, to embrace the lessons learned, adopt the good practices identified and build on the knowledge in existence.

This is why amongst the BiCIKL’s major final research outputs, there are two Policy Briefs meant to summarise and highlight important recommendations addressed to key policy makers, research institutions and funders of research. After all, it is the regulatory bodies that are best equipped to share and implement best practices and guidelines.

Most recently, the BiCIKL consortium published two particularly important policy briefs, both addressed to the likes of the European Commission’s Directorate-General for Environment; the European Environment Agency; the Joint Research Centre; as well as science and policy interface platforms, such as the EU Biodiversity Platform; and also organisations and programmes, e.g. Biodiversa+ and EuropaBON, which are engaged in biodiversity monitoring, protection and restoration. The policy briefs are also to be of particular use to national research funds in the European Union.

One of the newly published policy briefs, titled “Uniting FAIR data through interlinked, machine-actionable infrastructures”, highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data. The publication includes a list of recommendations addressed to policy-makers, as well as nine key action points. Understandably, amongst the main themes are those of wider international cooperation; inclusivity and collaboration at scale; standardisation and bringing science and policy closer to industry. Another major outcome of the BiCIKL project: the Biodiversity Knowledge Hub portal is noted as central to many of these objectives and tasks in its role of a knowledge broker that will continue to be maintained and updated with additional FAIR data-compliant services as a living legacy of the collaborative efforts at BiCIKL.

The second policy brief, titled “Liberate the power of biodiversity literature as FAIR digital objects”, shares key actions that can liberate data published in non-machine actionable formats and non-interoperable platforms, so that those data can also be efficiently accessed and used; as well as ways to publish future data according to the best FAIR and linked data practices. The recommendations highlighted in the policy brief intend to support decision-making in Europe; expedite research by making biodiversity data immediately and globally accessible; provide curated data ready to use by AI applications; and bridge gaps in the life cycle of research data through digital-born data. Several new and innovative workflows, linkages and integrative mechanisms and services developed within BiCIKL are mentioned as key advancements created to access and disseminate data available from scientific literature. 

While all policy briefs and factsheets – both primarily targeted at non-expert decision-makers who play a central role in biodiversity research and conservation efforts – are openly and freely available on the project’s website, the most important contributions were published as permanent scientific records in a BiCIKL-branded dedicated collection in the peer-reviewed open-science journal Research Ideas and Outcomes (RIO). There, the policy briefs are provided as both a ready-to-print document (available as supplementary material) and an extensive academic publication.

Currently, the collection: “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” in the RIO journal contains 60 publications, including policy briefs, project reports, methods papers, conference abstracts, demonstrating and highlighting key milestones and project outcomes from along the BiCIKL’s journey in the last three years. The collection also features over 15 scientific publications authored by people not necessarily involved in BiCIKL, but whose research uses linked open data and tools created in BiCIKL. Their publications were published in a dedicated article collection in the Biodiversity Data Journal.

BiCIKL keeps on adding project outcomes in own collection in RIO Journal

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Visit the Biodiversity Community Integrated Knowledge Library (BiCIKL) project’s website at: https://bicikl-project.eu/.

Don’t forget to also explore the Biodiversity Knowledge Hub (BKH) for yourself at: https://biodiversityknowledgehub.eu/ and watch the BKH’s introduction video. 

Highlights from the BiCIKL project are also accessible on Twitter/X from the project’s hashtag: #BiCIKL_H2020 and handle: @BiCIKL_H2020.

BiCIKL project sums up outcomes and future prospects at a Final GA in Cambridge

Brand new journal Estuarine Management and Technologies streamlines innovation in ecosystems conservation

There has been an increasing need to support the exchange of research related to the conservation and sustainable management of estuarine ecosystems by means of new-age technologies and approaches.

Where freshwater rivers meet seas and oceans lies a scientifically intriguing and ecologically important type of ecosystem. As estuarine ecosystems provide various and diverse services to humanity and the planet at large, including food security and natural buffers and filters in the events of storms and water pollution, there has been an increasing need to facilitate and support the exchange of research findings and ideas related to their conservation and sustainable management by means of new-age technology and novel approaches.

This is how a team of renowned and passionate scientists, headed by Dr. Soufiane Haddout (Ibn Tofail University, Morocco), took the decision to launch a brand new open-access, peer-reviewed scholarly, aptly titled Estuarine Management and Technologies. They explain the rationale behind the journal in a new editorial, published to mark the official launch of the journal.

Having already worked closely with the scientific publisher and technology provider Pensoft on the fine touches of the concept of the new academic title, the team opted to use Pensoft’s publishing platform of ARPHA. As a result, the new journal provides a seamless, end-to-end publishing experience, encompassing all stages between manuscript submission and article publication, indexation, dissemination and permanent archiving. 

Within the collaboration between the journal’s and Pensoft’s teams, Estuarine Management and Technologies will take advantage of various services offered by the ARPHA platform, including full-text automated export in machine-readable and minable JATS-XML format to over 60 relevant databases for scientific literature and data; semantically enriched and multimedia-friendly publications accessible in HTML; and rich statistics about the outreach and usage of each published article and its elements (e.g. figures and tables), including views, downloads, online mentions, and citations. 

The publishing platform’s in-house indexing team will continue their close work with the journal’s editors to ensure that the scholarly outlet retains highest quality and integrity, so that it covers the criteria for indexation at additional key databases that require individual evaluation. In the meantime, ARPHA’s technical and editorial teams will provide technical and customer support to authors, editors and reviewers. The marketing and promotion team of ARPHA will be also joining forces with the journal to boost the visibility and image of the new academic title.

During the launch phase, content accepted for publication following double-blinded peer review will be made public right away for free to both authors and readers, where the journal will be operating under a continuous publication model.

Estuarine Management and Technologies welcomes studies from a wide spectrum of disciplines, including physics, chemistry, geology, biology, and hydrology, with a focus on interdisciplinarity, multifaceted approaches and holistic perspectives.

“One crucial aspect of estuarine management is the sustainable use of resources to balance conservation with human needs. Striking this delicate equilibrium requires a holistic understanding of the intricate web of ecological interactions within estuarine environments. Advanced technologies, such as isotopic techniques, environmental DNA (eDNA) analysis, can provide insights into the biodiversity of estuarine ecosystems with unprecedented precision,”

explain Dr Haddout and his colleagues in the opening editorial.

Amongst the unique features of the new journal are several additional publication types, such as Expert View, Video Paper, Rapid Communication, Mini Review and Estuarine Scientists, where these have been added to traditional publication outputs (e.g. Research Paper, Review Paper, Data Paper) to foster collaboration between researchers and other stakeholders in the field.

The journal is also running an annual Trailblazing Talent in Estuarine Management and Technologies award intended to recognise and encourage young scientists and engineers at the forefront of cutting-edge research in estuarine management and technologies. Nominations and applications are currently open.

Estuarine Management and Technologies also welcomes applications for guest editors in order to further expand the journal and its immediate expert network.

“I am delighted to see the Estuarine Management and Technologies journal already live on the ARPHA platform. We are confident that this particularly important, yet so far quite overlooked area of study will greatly benefit from this highly promising journal,”

says Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

“I am pleased to announce the launch of the Estuarine Management and Technologies journal on ARPHA, a decision rooted in our commitment to advancing the field. We believe that this strategic partnership will not only enhance the visibility and accessibility of our journal, but will also foster collaboration and innovation within the estuarine management and technologies community. We expect this alliance to be a catalyst for scholarly excellence, providing a robust platform for researchers and practitioners to share insights, address challenges, and propel the field forward. Together with ARPHA, we are confident in the positive impact our journal will have on shaping the future of estuarine management and technologies.”

says Dr. Soufiane Haddout, Editor-in-Chief and founder, Estuarine Management and Technologies.

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You can visit the journal website and sign up for its newsletter from the homepage.

You can also follow Estuarine Management and Technologies on X (formerly Twitter).

Maximising the impact of standardised biodiversity data: Pensoft’s role in the EU project B-Cubed

In line with its commitment to providing open-access biodiversity data, Pensoft has joined forces with 12 organisations to form the B-Cubed project.

The problem at hand

Measuring the extent and dynamics of the global biodiversity crisis is a challenging task that demands rapid, reliable and repeatable biodiversity monitoring data. Such data is essential for policymakers to be able to assess policy options effectively and accurately. To achieve this, however, there is a need to enhance the integration of biodiversity data from various sources, including citizen scientists, museums, herbaria, and researchers.

B-Cubed’s response

B-Cubed (Biodiversity Building Blocks for policy) hopes to tackle this challenge by reimagining the process of biodiversity monitoring, making it more adaptable and responsive. 

B-Cubed’s approach rests on six pillars: 

  • Improved alignment between policy and biodiversity data. Working closely with existing biodiversity initiatives to identify and meet policy needs.
  • Evidence base. Leveraging data cubes to standardise access to biodiversity data using the Essential Biodiversity Variables framework. These cubes are the basis for models and indicators of biodiversity.
  • Cloud computing environment. Providing users with access to the models in real-time and on demand.
  • Automated workflows. Developing exemplary automated workflows for modelling using biodiversity data cubes and for calculating change indicators.
  • Case studies. Demonstrating the effectiveness of B-Cubed’s tools.
  • Capacity building. Ensuring that the solutions meet openness standards and training end-users to employ them.

Pensoft’s role

Harnessing its experience in the communication, dissemination and exploitation of numerous EU projects, Pensoft focuses on maximising B-Cubed’s impact and ensuring the adoption and long-term legacy of its results. This encompasses a wide array of activities, ranging all the way from building the project’s visual and online presence to translating its results into policy recommendations. Pensoft also oversees B-Cubed’s data management by developing a Data Management Plan which ensures the implementation of the FAIR data principles and maximises the access to and re-use of the project’s research outputs.

Full list of partners

Visit B-Cubed’s website at https://b-cubed.eu/. You can also follow the project on X @BCubedProject and LinkedIn /B-Cubed Project, as well as by subscribing to its newsletter here.

Celebrating ZooKeys: 15 years of taxonomic excellence

We look back on this incredible journey with pride and appreciation for the countless researchers, authors, reviewers, and supporters who have helped make this dream a reality.

Today, we are thrilled to share with you the celebration of a remarkable milestone in our journey. In July, we marked our 15th birthday – a decade and a half of fostering the free exchange of ideas, data, and knowledge in the vast realm of zoology.

We look back on this incredible journey with pride and appreciation for the countless researchers, authors, reviewers, and supporters who have helped make this dream a reality. From the very inception, our goal has been to create a platform where zoological discoveries can shine brightly, accessible to all who share a passion for the wonders of the animal kingdom.

ZooKeys was born out of our collective desire to push the boundaries of scientific publishing, to embrace innovation, and to provide a space where the brightest minds in zoology could come together. Over the years, we have not only achieved this but, thanks to our publisher Pensoft, have also become pioneers in implementing cutting-edge technologies to enhance the way knowledge is shared and absorbed.

ZooKeys was the first of Pensoft’s open-access journals, set up to accelerate research and free information exchange in taxonomy, phylogeny, biogeography and evolution of animals. Starting as a taxonomic journal, it quickly expanded to other zoology-related sciences, such as ecology, molecular biology, genomics, evolutionary biology, palaeontology, behavioural science, bioinformatics etc… The journal has been thriving since its inception and is currently considered as one of the most prolific and liked Open Access journals in zoology. 

Erwin T, Stoev P, Penev L (2018) ZooKeys anniversary: 10 years of leadership toward open-access publishing of zoological data and establishment at Pensoft of like-minded sister journals across the biodiversity spectrum. ZooKeys 770: 1-8. https://doi.org/10.3897/zookeys.770.28105

One of our proudest achievements was being the first taxonomic journal to introduce semantic tagging and content enhancements, revolutionizing the way information is presented and accessed. This endeavor, which began with our 50th issue in 2010, marked a turning point in scholarly publishing.

The cover of the first issue of ZooKeys.

As of today, we’ve published more than 180,000 pages of research in almost 7,000 articles that have amassed more than 3 million views. Here is a Top 5 of our most popular articles ever:

  • Helgen K, Pinto M, Kays R, Helgen L, Tsuchiya M, Quinn A, Wilson D, Maldonado J (2013) Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito. ZooKeys 324: 1-83. https://doi.org/10.3897/zookeys.324.5827, with 80,500 views,
  • Bousquet Y (2016) Litteratura Coleopterologica (1758–1900): a guide to selected books related to the taxonomy of Coleoptera with publication dates and notes. ZooKeys 583: 1-776. https://doi.org/10.3897/zookeys.583.7084 with 69,543 views,
  • Ledford J, Griswold C, Audisio T (2012) An extraordinary new family of spiders from caves in the Pacific Northwest (Araneae, Trogloraptoridae, new family). ZooKeys 215: 77-102. https://doi.org/10.3897/zookeys.215.3547 with 65,446 views,
  • Ibrahim N, Sereno PC, Varricchio DJ, Martill DM, Dutheil DB, Unwin DM, Baidder L, Larsson HCE, Zouhri S, Kaoukaya A (2020) Geology and paleontology of the Upper Cretaceous Kem Kem Group of eastern Morocco. ZooKeys 928: 1-216. https://doi.org/10.3897/zookeys.928.47517 with 64,456 views,
  • Bouchard P, Bousquet Y, Davies A, Alonso-Zarazaga M, Lawrence J, Lyal C, Newton A, Reid C, Schmitt M, Slipinski A, Smith A (2011) Family-Group Names In Coleoptera (Insecta). ZooKeys 88: 1-972. https://doi.org/10.3897/zookeys.88.807 with 63,524 views.

Our journey would have been incomplete without you – our avid readers and supporters. Your hunger for knowledge, your curiosity, and your unwavering support have been the wind beneath our wings, motivating us to do better, and reinforcing the importance of what we do. As we celebrate our 15th birthday, we extend our deepest gratitude to each one of you who has been a part of our history.

Part of an illustration by Nancy Halliday from the most popular ZooKeys paper to date.

Looking ahead, the future of ZooKeys looks as bright as ever. We are committed to continuing our legacy of innovation, collaboration, and accessibility. Our goal remains steadfast – to be a beacon of knowledge, a platform that fosters discoveries, and a source of inspiration for the next generation of zoological minds.

As we celebrate our 15th anniversary, we are filled with a sense of awe and wonder at the remarkable achievements we have collectively made. Thank you for being a part of this incredible journey. Here’s to the next  15 years and beyond, as we continue to explore, discover, and celebrate the extraordinary diversity of life on Earth.

A decade of empowering biodiversity science: celebrating 10 years of Biodiversity Data Journal

Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.

Today, 16 September 2023, we are celebrating our tenth anniversary: an important milestone that has prompted us to reflect on the incredible journey that Biodiversity Data Journal (BDJ) has been through.

From the very beginning, our mission was clear: to revolutionise the way biodiversity data is shared, accessed, and harnessed. This journey has been one of innovation, collaboration, and a relentless commitment to making biodiversity data FAIR – Findable, Accessible, Interoperable, and Reusable.

Over the past 10 years, BDJ, under the auspices of our esteemed publisher Pensoft, has emerged as a trailblazing force in biodiversity science. Our open-access platform has empowered researchers from around the world to publish comprehensive papers that seamlessly blend text with morphological descriptions, occurrences, data tables, and more. This holistic approach has enriched the depth of research articles and contributed to the creation of an interconnected web of biodiversity information.

In addition, by utilising ARPHA Writing Tool and ARPHA Platform as our entirely online manuscript authoring and submission interface, we have simplified the integration of structured data and narrative, reinforcing our commitment to simplifying the research process.

One of our most significant achievements is democratising access to biodiversity data. By dismantling access barriers, we have catalysed the emergence of novel research directions, equipping scientists with the tools to combat critical global challenges such as biodiversity loss, habitat degradation, and climate fluctuations.

We firmly believe that data should be openly accessible to all, fostering collaboration and accelerating scientific discovery. By upholding the FAIR principles, we ensure that the datasets accompanying our articles are not only discoverable and accessible, but also easy to integrate and reusable across diverse fields.

As we reflect on the past decade, we are invigorated by the boundless prospects on the horizon. We will continue working on to steer the global research community towards a future where biodiversity data is open, accessible, and harnessed to tackle global challenges.

Ten years of biodiversity research

To celebrate our anniversary, we have curated some of our most interesting and memorable BDJ studies from the past decade.

  • Recently, news outlets were quick to cover a new species of ‘snug’ published in our journal.
New ‘snug,’ a snail with a too-small shell, described from Brunei rainforest
  • This Golden Retriever trained to monitor hermit beetle larvae proved once again the incredible capabilities of our canine friends.
Teseo, the Golden Retriever monitoring hermit beetle larvae
  • Who could forget this tiny fly named after the former Governor of California?
  • Or this snail named after climate activist Greta Thunberg?
Craspedotropis gretathunbergae

New discoveries are always exciting, but some of our favourite research focuses on formerly lost species, back where they belong.

  • Like the griffon vulture, successfully reintroduced to Bulgaria after fifty years.
The incredible return of Griffon Vulture to Bulgaria’s Eastern Balkan Mountains

Citizen science has shown time and time again that it holds an important position in biodiversity research.

  • This group, for example, who found a beetle the size of a pinhead in Borneo.
“Life Beneath the Ice”, a short musical film about light and life beneath the Antarctic sea-ice by Dr. Emiliano Cimoli

We extend our heartfelt gratitude to our authors, reviewers, readers, and the entire biodiversity science community for being integral parts of this transformative journey. Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.

Follow BDJ on social media:

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Transformative changes for biodiversity and climate protection: Pensoft partners with EU project TRANSPATH

As an expert in science communication, dissemination and exploitation, Pensoft joins TRANSPATH for transformative changes at consumer, producer and organisational levels.

As an expert in science communication, dissemination and exploitation, Pensoft joins the Horizon-funded project TRANSPATH to identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels.

Why TRANSPATH?

The magnitude of biodiversity loss and climate crisis has grown exponentially in recent years, which will inevitably lead to serious consequences at a global scale. Although reversing the degradation of ecosystems and reducing greenhouse gas emissions are top priorities for the European Union, science and policy communities are united in the belief that conventional policies alone are not enough to halt biodiversity loss or mitigate climate change.

In order to achieve climate neutrality by 2050, whilst simultaneously reshaping people’s relations with nature, we need transformative changes in our economies and societies urgently. 

How?

TRANSPATH (short for TRANSformative PATHways for synergising just biodiversity and climate actions) – a new European Union-funded project, plans to satisfy this need by accelerating diverse transformative pathways towards biodiversity-positive and climate-proofed societies, with sensitivity to social-cultural contexts and rights.

TRANSPATH will identify leverage points and interventions for triggering transformative changes at consumer, producer and organisational levels. A research team, consisting of leading academics, science-policy experts, and early-career professionals, will directly engage with diverse stakeholders, who affect and are affected by trade regimes and associated ‘greening’ mechanisms.

As a leader of WP5: Dissemination, outreach and catalysing transformative pathways, Pensoft is responsible for providing a dissemination and communication strategy, as well as taking care of the project branding and website. In addition, the Pensoft team is to organise joint activities with other projects or initiatives on transformative change and related topics.

What?

Funded by the European Union’s Horizon Europe research and innovation programme, TRANSPATH was launched on 1st November 2022 and will be running until October 2026. The official kick-off of the project took place online and was followed by an in-person kick-off meeting of all consortium members on the 2nd and 3rd February 2023 in Wageningen, the Netherlands.

For the next four years TRANSPATH will be focussing on the design and integrated assessment of a suite of transformative pathways that hold potential to accelerate shifts in unsustainable patterns of extraction, production, consumption and trade. The project’s mission will be achieved by four objectives:

  1. Set up a Policy Board and Science-policy-practitioner Labs at multiple scales to engage and jointly deliberate on implications of diverse visions and pathways of change.
  2. Identify and characterise leverage points for diverse contexts that lead to positive synergies between biodiversity, climate and trade domains.
  3. Integrate and customise European and global pathways by considering coupled biodiversity-climate actions and critical leverage points.
  4. Identify and test alternative interventions at global and European scales that can trigger transformative change at the level of consumers, producers and organisations.

TRANSPATH will bring together and advance several strands of recent research, which hold potential for triggering and accelerating transformative changes that can restrain biodiversity loss and climate change. 

The project will draw on diverse contexts in Eastern and Western Europe, Africa and Latin America, to engage with policy makers and practitioners, individuals, Civil Society Organisations (CSOs), small- and medium-sized enterprises (SMEs) and multinational corporations.

In addition, policy packages and other interventions will be designed to facilitate the emergence of leverage points at different scales of action in ways that change the decision-making framework of everyday choices.

These interventions take into account the synergies and trade-offs of actions across multiple individuals and locations, as well as the role of incentives and political obstacles to implementation.

The EU project will provide a suite of Transformative Pathways along with a Toolbox of Transformative Interventions to trigger and enable these pathways. The Transformative Navigation Toolkit assists practitioners in enabling and navigating these pathways, acknowledging that determining what constitutes a ‘transformative pathway’ is also a product of an iterative and adaptive process that emerges and evolves over time.

Whom?

The TRANSPATH project brings together leading academics, science-policy experts, and young professionals from different social-cultural origins across Eastern and Western Europe, Africa and Latin America. Represented by nine countries and twelve nationalities, the consortium comprises a diverse range of scientific disciplines in environments, economics, and social sciences.

Dedicated to ensuring sufficient engagement from local to global levels in this project, the experts are focused on integrated and inclusive deliberation that is essential for identifying, legitimising, and navigating transformative pathways.

Full list of partners

You can find more about the project on the TRANSPATH website: transpath.eu. Stay up to date with the project’s progress on Twitter (@TRANSPATH_EU) and Linkedin (/transpath-project).

BiCIKL Project supports article collection in Biodiversity Data Journal about use of linked data

Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data

The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications* submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge. 

BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.

Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.

The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions, and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

To be eligible for the collection, a manuscript must comply with at least two of the conditions listed below. In the submission form, the author needs to specify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.

All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 

The data used in the articles must comply with the Data Quality Checklist and Fair Data Checklist available in the Authors’ instructions of the journal.

Conditions for publication in the article collection:

  • The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)

  • Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.

  • Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.

  • Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.

  • More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin. 

  • In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision or catalogue. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.

  • Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.

  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.

  • Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.

  • Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.

  • Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
  • Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.

We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection: 

Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data: 

(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?

(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined? 

(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)? 

(4) How could research data and narratives be re-used to support more extensive and data-rich studies? 

(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?

All manuscripts submitted to the Biodiversity Data Journal have their data audited by data scientists prior to the peer review stage.

Once published, specimen records data are being exported in Darwin Core Archive to GBIF.

The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.

All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.

* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.

Follow the BiCIKL Project on Twitter and Facebook. Join the conservation on via #BiCIKL_H2020.

You can also follow Biodiversity Data Journal on Twitter and Facebook.

Tag team: a tale of two Antarctic blue whales

For the first time, the satellite tracks of two Antarctic blue whales, tagged a decade ago, have been published in the open-access Biodiversity Data Journal.

Ten years ago, Dr Virginia Andrews-Goff was riding the bowsprit of a six-metre boat, as a 30-metre, 120-tonne Antarctic blue whale surfaced alongside.

That day in the Southern Ocean, she became the first and, so far, the only person, to deploy satellite tags on two of these critically endangered and rarely sighted giants.

Scientists approach a 30 metre blue whale in their six metre boat. ©Kylie Owens/Australian Antarctic Division

At the time, her success added weight to a case in the United Nations International Court of Justice, demonstrating that scientific research on whales could be conducted without killing them.

Dr Andrews-Goff and her colleagues at the Australian Antarctic Division have now published the two satellite tracks generated by that 2013 work, in the open-access Biodiversity Data Journal.

This is a unique data set that was incredibly challenging to get.

Dr Virginia Andrews-Goff

The tracks give an insight into the animals’ movement and behaviour on their feeding grounds, and illustrate the significant logistical challenges needed to successfully locate, tag, and track Antarctic blue whales.

“This is a unique data set that was incredibly challenging to get, and, unfortunately, for 10 years no-one has been able to generate more data,” Dr Andrews-Goff said.

“We know very little about the movement and distribution of Antarctic blue whales, where they migrate, where they forage and breed, and we don’t understand the threats they might face as they recover from whaling.”

Two satellite tagged Antarctic blue whales have provided the first insights into the movement and behaviour of these critically endangered ocean giants on their feeding grounds. ©Australian Antarctic Division

Part of the issue is that the animals are incredibly difficult to find. Commercial whaling in the 1960s and ‘70s killed about 290,000 Antarctic blue whales, accounting for 90% of the population. By the late 1990s, the world’s population of Antarctic blue whales was estimated at 2280 animals.

Back in 2013, the research team used novel acoustic tracking techniques to detect blue whale calls and hone in on their location from up to 1000 kilometres away. Once the whales were in sight (in two separate locations), an expert crew manoeuvred close to their fast-moving targets.

The satellite tags showed that the whales travelled 1390 kilometres in 13 days and 5550 kilometres in 74 days, with an average distance of more than 100 kilometres per day.

“The two whales did entirely different things, but what became obvious is that these animals can travel really quickly,” Dr Andrews-Goff said.

“If you consider how far and fast these animals moved, protecting the broader population against potential threats will be tricky because they could potentially circumnavigate Antarctica within a single feeding season.”

his map shows the movement of two satellite tagged Antarctic blue whales. The track on the bottom right are the movements of one whale over 13 days. The other three tracks capture segments of movement by the second whale over 74 days. The tag for this second whale did not transmit data consistently, resulting in data gaps throughout the tracking period.
The blue portions of track show where the whales were moving quickly and directly, suggesting they were in transit, while the orange locations show where they slowed down and appeared to be searching or foraging.    ©Australian Antarctic Division

Since the tracks were obtained, new analytical methods have added some behavioural context to the data.

Two movement rates were observed – a faster ‘in transit’ speed averaging 4.2 km/hr and a slower speed of 2.5 km/hr, thought to correspond with searching or foraging.

“It looks like the whales might hang around in one area to feed and then move quickly to another area and hang around there for another feed,” Dr Andrews-Goff said.

“There may be certain areas that are better feeding grounds than others. From a management perspective, it would be good to understand what is it that makes these areas important?”

Even at a sample size of two, Dr Andrews-Goff said the satellite tracks will assist the International Whaling Commission’s management of Antarctic blue whales, by providing initial insights into blue whale foraging ecology, habitat preferences, distribution, movement rates, and feeding. These will inform an in-depth assessment of Antarctic blue whales due to begin in 2024.

Original source:

Andrews-Goff V, Bell EM, Miller BS, Wotherspoon SJ, Double MC (2022). Satellite tag derived data from two Antarctic blue whales (Balaenoptera musculus intermedia) tagged in the east Antarctic sector of the Southern Ocean. Biodviersity Data Journal 10: e94228 https://doi.org/10.3897/BDJ.10.e94228

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