Pensoft launches ORPHO: A new intelligent workspace for scientific writing

The beta release of an innovative collaborative stand-alone authoring tool transforms manuscript preparation with semantic enrichment and real-time collaboration capabilities.

Scholarly publisher and technology provider Pensoft Publishers announces the beta launch of ORPHO, a revolutionary online platform designed to streamline collaborative scientific writing and produce AI-ready, future-proof scholarly literature. 

ORPHO presents a significant advancement in scholarly publishing technology, combining intuitive writing features with sophisticated semantic enrichment capabilities. The new platform builds upon Pensoft’s fifteen years of experience as a developer of semantic publishing infrastructure.

Key Features

Within a shared online workspace, researchers can start with built-in customisable templates, create their own or import an existing file. They can then team up with collaborators in real time using track changes, role-based user rights, inline comments, and document-level chat. More significantly, ORPHO automatically structures scientific content according to international publishing standards, making research outputs findable, discoverable, interoperable and reusable (FAIR) once published. 

Unlike its predecessor, the ARPHA Writing Tool, ORPHO is available as a standalone real-time collaborative workspace decoupled from journals hosted on Pensoft’s ARPHA Publishing Platform. Once a manuscript is ready, authors receive AI-FAIR machine-readable content that can be formatted to meet multiple journal requirements at the click of a button.

The platform’s adaptability to domain-specific workflows is currently being piloted in biodiversity science. ORPHO integrates seamlessly with leading biodiversity data aggregators, including the Global Biodiversity Information Facility (GBIF), Barcode of Life Data Systems (BOLD) and PlutoF, via import and export facilities for structured data, making ORPHO particularly valuable for researchers handling taxonomic, ecological and biodiversity data. 

Taxon names, for example, can be automatically imported and linked through persistent identifiers from sources like the Catalogue of Life (CoL), International Plant Names Index (IPNI), World Register of Marine Species (WoRMS) and World Flora Online (WFO).

Why ORPHO?

The name draws inspiration from multiple sources which reflect the tool’s philosophy and heritage. Named after Orphium: a unique plant genus endemic to South Africa whose sole species (Orphium frutescens) is known as the sea rose, ORPHO reflects the platform’s distinctive nature, heritage, and core philosophy.

It also evokes Orpheus, the legendary musician of ancient Thrace whose home region, the Rhodopi Mountains, lies in present-day Bulgaria, where ORPHO’s developer, Pensoft, is headquartered. The name thus honours the tool’s origins whilst embodying the exceptional creative performance it enables. 

***

Prof. Dr. Lyubomir Penev, founder and CEO of Pensoft, comments:

“We are well aware that researchers today face an overwhelming list of formatting requirements and technical demands in an AI-driven landscape. It is true that rapid technological advancement presents both immense opportunities and mounting complexities for researchers.

We built ORPHO to remove that friction by offering an intuitive, collaborative workspace that lets scientists focus on their research. As a scientific publisher, our mission is to make scholarly publishing a seamless, rewarding experience fit for the modern age.”

The beta release invites researchers, institutions and publishing platforms to trial ORPHO and provide feedback. Access is available at orpho.net.

Pensoft awarded the FAO AGRIS Seal of Recognition for 2027

The seal recognises institutions that consistently share open-access agricultural research with the global community.

Pensoft has been awarded the Seal of Recognition for the FAO AGRIS Active Data Provider of the Year for 2027. The seal is granted by the Food and Agriculture Organisation of the United Nations through its AGRIS initiative, and it recognises institutions that consistently share open-access agricultural research with the global community.

Notably, Pensoft joined the FAO AGRIS network back in 2024, and the organisation has renewed our seal every year since, a recognition we’re proud to have kept.

What has changed is the scale of our contribution. In 2024, Pensoft’s records on AGRIS numbered just under 15,000. Today, that figure has doubled to nearly 30,000, drawn from all 51 of our journals that fall within the scope of FAO AGRIS. The subjects covered are wide-ranging, spanning taxonomy, biodiversity, conservation and biogeography – these are all areas that feed directly into sustainable agriculture and natural resource management.

Through AGRIS, this research travels well beyond our own journals to researchers, policymakers and practitioners worldwide, adding to the shared pool of open knowledge that supports global food security and environmental sustainability. We’re glad to keep contributing to that effort, and look forward to continuing our work with FAO AGRIS in the years to come.


About FAO

The Food and Agriculture Organisation (FAO) is a specialised agency of the United Nations that leads international efforts to defeat hunger. Its goal is to achieve food security for all, ensuring that people have regular access to enough high-quality food to lead active, healthy lives. With 194 members, 193 countries and the European Union, FAO works in over 130 countries worldwide.

About Pensoft

Founded in 1992 “by scientists, for scientists,” Pensoft is an academic open-access publishing company well known worldwide for its cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials. In 2010, Pensoft became the first scientific publisher to introduce semantic enrichments in scholarly publications. Through its Research and Technical Development department, the company is involved in a range of research and technology projects.

Pensoft and the Vietnam Academy of Science and Technology forge new scholarly partnership

At a visit at the publisher’s headquarters the two parties signed a Memorandum of Understanding.

In August, Pensoft had the honour of welcoming colleagues from the Vietnam Academy of Science and Technology (VAST) to the headquarters of the open-access scholarly publisher and technology provider in Sofia, Bulgaria. The visit was marked by engaging discussions on scholarly publishing, future innovations, current challenges in academia and potential collaborations.

The highlight of the meeting was the formal signing of a Memorandum of Understanding (MoU) between Prof. Dr. Lyubomir Penev, Pensoft’s CEO and founder, and Prof. Dr. Thai Hoang, Vice Chairman of the Scientific Council of Materials Science at VAST and the Editor‑in‑Chief of the Vietnam Journal of Science and Technology.

“This Memorandum of Understanding marks an important step towards fostering international collaboration in scholarly publishing. By combining the expertise and know-how of Pensoft and VAST, we aim to make research more accessible and innovative for communities worldwide,”

commented Prof. Dr. Lyubomir Penev.

“I am very happy to visit Bulgaria and collaborate with Pensoft Publishers. Here, we know Pensoft and the ARPHA publishing platform for their diverse publishing solutions designed for scientific papers, monographs, academic books and more, as well as their professional and efficient work. All this makes them quite prestigious for us.

Starting from this Memorandum of Understanding, next, we will explore ways to use the ARPHA publishing platform for the publication of Vietnam’s scientific journals, books and other research outputs.”

added Prof. Dr. Thai Hoang.

Over the course of the visit, the group engaged in an enriching dialogue. Guests from VAST offered an in-depth look at their publication outlets and shared insights into the Vietnamese scholarly publishing landscape, as well as the nation’s rich cultural heritage and natural wonders. 

In turn, Pensoft offered a comprehensive overview of the company’s journey of over three decades, starting from the launch of the first Pensoft journals and proceeding to the continuous development of several innovative publication platforms and solutions, including the full-featured end-to-end publishing platform ARPHA. Today, there are over 80 open-access peer-reviewed journals, including both Pensoft-launched titles, and many owned and run by research institutions, universities and learned societies from around the globe.

The visit continued beyond the office with the publisher’s management inviting their guests to a several-day trip around the country that covered the cultural and historic hubs of Plovdiv and Koprivshtitsa.

By the end of the visit, both parties agreed that their meeting in Bulgaria underscores their shared vision: to advance open, innovative, and accessible scholarly communication. With the MoU in place, both sides look forward to transforming this mutual understanding into concrete collaborative initiatives.

*

With perfect timing, shortly after the visit, one of the VAST delegates: biologist Prof. Dr. Quang Manh Vu (also affiliated with the Hoa Binh University, Hanoi, Vietnam), in collaboration with his Bulgarian and Vietnamese colleagues: Dr. Ivailo Dedov (Bulgarian Academy of Sciences) and Dr. Tuan Trieu Anh (Hung Vuong University, Viet Tri City, Vietnam) published a study in Pensoft’s inaugural and flagship journal in zoological systematics: ZooKeys. The research paper lists species of slugs and semi-slugs of the superfamily Helicarionoidea the team collected in North Vietnam in 2023. Amongst the collected specimens, the scientists discovered a new-to-science species of semi-slug they named after Pensoft’s Prof. Dr. Lyubomir Penev, who is himself a biologist and taxonomist by background. 

“When I found out I had a new species, I had no hesitation on the name: Ostracolethe penevi. I had been looking forward to naming a curious species after my friend Prof. Lyubomir Penev, a man who made the world look up to Bulgarian science, and someone who has helped me a lot through the years,”

comments Dr. Ivailo Dedov in a news announcement.

“This newly described species deserves a name that reflects the generosity of nature, the advancement of science, and the enduring friendship between Vietnam and Bulgaria,”

added Prof. Dr. Quang Manh Vu.

***

Additional information:

About Vietnam Academy of Science and Technology (VAST):

Founded on 20 May 1975, VAST is Vietnam’s largest multidisciplinary research organization, with branches in Hanoi, Ho Chi Minh City, Haiphong, Nha Trang, Dalat, and Hue. Its mission spans basic and applied research, the development of high technology, human resource training, and providing scientific advice to the government on pressing national issues. 

VAST is known for achieving high output in international peer-reviewed journals; in 2023, more than 2,200 works were published, with nearly 80% in international outlets. The Academy is responsible for several cutting-edge initiatives, including satellite R&D through the Vietnam National Space Center, strategic technology fields aligned with the Fourth Industrial Revolution (e.g. AI, new materials, semiconductors), and large-scale environmental and biodiversity monitoring across the country. Looking forward, VAST has set ambitious goals, including mastering key advanced technologies, increasing technology transfer, enhancing publication impact, strengthening partnerships at home and abroad, and cultivating world-class scientific talent.

The Biodiversity Data Journal launches its own data portal on GBIF

With this simple website designed to lower technical demands, data managers and other stakeholders can easily focus on data exploration and reuse.

The Biodiversity Data Journal (BDJ) became the second open-access peer-reviewed scholarly title to make use of the hosted portals service provided by the Global Biodiversity Information Facility (GBIF): an international network and data infrastructure aimed at providing anyone, anywhere, open access to data about all types of life on Earth. 

The Biodiversity Data Journal portal, hosted on the GBIF platform, is to support biodiversity data use and engagement at national, institutional, regional and thematic scales by facilitating access and reuse of data by users with various expertise in data use and management. 

Having piloted the GBIF hosted portal solution with arguably the most revolutionary biodiversity journal in its exclusively open-access scholarly portfolio, Pensoft is to soon replicate the effort with at least 20 other journals in the field. This would mean that the publisher will more than double the number of the currently existing GBIF-hosted portals.

As of the time of writing, the BDJ portal provides seamless access and exploration for nearly 300,000 occurrences of biological organisms from all over the world that have been extracted from the journal’s all-time publications. In addition, the portal provides direct access to more than 800 datasets published alongside papers in BDJ, as well as to almost 1,000 citations of the journal articles associated with those publications.  

The release of the BDJ portal should inspire other publishers to follow suit in advancing a more interconnected, open and accessible ecosystem for biodiversity research

Vince Smith

Using the search categories featured in the portal, users can narrow their query by geography, location, taxon, IUCN Global Red List Category, geological context and many others. The dashboard also lets users access multiple statistics about the data, and even explore potentially related records with the help of the clustering feature (e.g. a specimen sequenced by another institution or type material deposited at different institutions). Additionally, the BDJ portal provides basic information about the journal itself and links to the news section from its website. 

A video displaying an interactive map with occurrence data on the BDJ portal.

Launched in 2013 with the aim to bring together openly available data and narrative into a peer-reviewed scholarly paper, the Biodiversity Data Journal has remained at the forefront of scholarly publishing in the field of biodiversity research. Over the years, it has been amongst the first to adopt many novelties developed by Pensoft, including the entirely XML-based ARPHA Writing Tool (AWT) that has underpinned the journal’s submission and review process for several years now. Besides the convenience of an entirely online authoring environment, AWT provides multiple integrations with key databases, such as GBIF and BOLD, to allow direct export and import at the authoring stage, thereby further facilitating the publication and dissemination of biodiversity data. More recently, BDJ also piloted the “Nanopublications for Biodiversity” workflow and format as a novel solution to future-proof biodiversity knowledge by sharing “pixels” of machine-actionable scientific statements.   

“I am thrilled to see the Biodiversity Data Journal’s (BDJ) hosted portal active, ten years since it became the first journal to submit taxon treatments and Darwin Core occurrence records automatically to GBIF! Since its launch in 2013, BDJ has been unrivalled amongst taxonomy and biodiversity journals in its unique workflows that provide authors with import and export functions for structured biodiversity data to/from GBIF, BOLD, iDigBio and more. I am also glad to announce that more than 30 Pensoft biodiversity journals will soon be present as separate hosted portals on GBIF thanks to our long-time collaboration with Plazi, ensuring proper publication, dissemination and re-use of FAIR biodiversity data,” said Prof. Dr. Lyubomir Penev, founder and CEO of Pensoft, and founding editor of BDJ.

“The release of the BDJ portal and subsequent ones planned for other Pensoft journals should inspire other publishers to follow suit in advancing a more interconnected, open and accessible ecosystem for biodiversity research,” said Vince Smith, editor-in-chief of BDJ and head of digital, data and informatics at the Natural History Museum, London.

Meet the Libroscope: a new vision for ‘liberating’ data from biodiversity publications

Pensoft is among the first signatories dedicated to fully leveraging biodiversity knowledge from research publications within an open science framework by 2035

Some of the world’s leading institutions, experts and scientific infrastructures relating to biodiversity information are uniting around a new 10-year roadmap to ‘liberate’ data presently trapped in research publications.

The initiative aims to enable the creation of a ‘Libroscope’ – a mechanism for unlocking and linking data from scientific literature to support understanding of biodiversity, as the microscope and telescope previously revolutionized science. The plan largely builds on existing technology and workflows, and does not rely on construction of a new technical infrastructure.

The proposals result from a symposium involving 51 experts from 10 countries held in August 2024 at the 7th-century monastery at Disentis in the Swiss Alps, supported financially by the Arcadia Fund. The symposium was a 10-year follow-up to the 2014 meeting at Meise Botanic Garden in Belgium, which led to the Bouchout Declaration on open biodiversity knowledge management. The Disentis meeting evaluated progress since then, and identified priorities for the decade ahead.

Group photo from the Disentis meeting (Switzerland, August 2024).

While acknowledging major advances in the sharing and use of open biodiversity data, the participants noted that accessing data within research publications is often very cumbersome, with databases disconnected from each other and from the source literature. Liberating and linking data from such publications – estimated to encompass more than 500 million total pages – would represent a compelling mission for the next decade.

Achieving this mission will support further research, and understanding of biodiversity vital to meeting global goals and targets such as the Kunming Montreal Global Biodiversity Framework (KMGBF), as well as assisting the compiling of knowledge assessments such as those carried out by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES).

A roadmap for staged action over the next decade was agreed by the symposium participants, with the following vision: “By 2035, the power of biodiversity knowledge from research publications will be fully leveraged within an open science framework, including unencumbered data discovery, access, and re-use across scientific disciplines and policy applications.

The ‘Disentis Roadmap’, further developed following the symposium, and now released publicly, has already been signed by 26 institutions and a further 46 individual experts on five continents – among them major natural history collections such as Meise Botanic Garden, Botanic Garden and Botanical Museum Berlin, the National Museum of Natural History in Paris, and Royal Botanic Gardens, Kew; infrastructures such as the Global Biodiversity Information Facility (GBIF), Biodiversity Heritage Library (BHL), Catalogue of Life, LifeWatch ERIC and the Swiss Institute of Bioinformatics (SIB); journal publishers such as Pensoft Publishers and the European Journal of Taxonomy; research institutions such as Chinese Academy of Sciences and the Senckenberg Society for Nature Research; and networks such as TDWG Biodiversity Information Standards and Consortium of European Taxonomic Facilities (CETAF). See the full list of signatories here.

The roadmap remains open for further signatures, ahead of the launch of an action plan at the Living Data conference in Bogotá, Colombia in October 2025. The original signatories hope that a much broader group of institutions and individuals, across global regions and disciplines, will join the initiative and help to shape implementation of its vision. Engagement of funders will also be critical to realize its objectives.

The specific goals of the roadmap are that by 2035:

  • All major public biodiversity research funders and academic publishers will encourage and enable publication of data adhering to the FAIR principles (findable, accessible, interoperable and reusable);
  • Biodiversity-focussed publications will be accessible in machine-actionable formats, with all non-copyrightable parts of articles flowing into public data repositories;
  • Published research on biodiversity will be ‘fully AI-ready’, that is openly available for AI training and properly labelled for ingestion by machine-learning modelled, within appropriate ethical and legal frameworks;
  • Dedicated funding from research and infrastructure grants will be reserved for ensuring access to biodiversity data and knowledge.

“We finally have a chance to make a quantum leap in understanding and monitoring biodiversity, by leveraging the power of digital technologies, and combining modern genomic methods with the vast amount of research data published daily and currently stuck in the publication prison. The ‘Libroscope’ will help to explore the universe of existing knowledge, accumulated over hundreds of years, and bring it to the forefront of developments in the digital age, helping nature and people across the globe.”

commented Donat Agosti of the Swiss organization Plazi, who convened the Disentis symposium.

A recent demonstration of the principles of the ‘Libroscope’ was the launch of data portals for the European Journal of Taxonomy (EJT) and the Biodiversity Data Journal, as part of the GBIF hosted portal programme. The new portals showcase the data contained within taxonomic literature published by the journals, making use of the workflow originally developed by Plazi and partners to extract re-usable data from articles traditionally locked in static PDF files. Once created, these data objects then flow into platforms such as GBIF, Catalogue of Life, ChecklistBank and the BiodiversityPMC, and are stored in the Biodiversity Literature Repository at Zenodo hosted by CERN. This process enables data on new species and the location of related specimens cited in the literature to be openly accessible in near-real time, and available for long-term access.

The newly launched Biodiversity Data Journal data portal is part of the GBIF-hosted portal programme. It showcase the data contained within taxonomic literature published by the journal.

“As a publisher of dozens of renowned academic journals in the field of biodiversity and systematics with experience in technology development, at Pensoft, we have always recognised the key role of academic publishers in scholarly communication. It’s not only about publishing the latest research. Above all, it’s about putting scientific work in the hands of those who need it: be it future researchers, policy-makers or their AI-powered assistants. Now that the Disentis roadmap is already a fact, we hope that many others will also join us on this ambitious journey to open up the knowledge we have today for those who will need it tomorrow.”

said Prof. Dr. Lyubomir Penev, founder and CEO at Pensoft, who attended the Disentis symposium.

“By repositioning scientific publications as an essential part of the research cycle, the Disentis Roadmap encourages publishers and the scientific community to move beyond open access towards FAIR access. Proactively ensuring data quality and dissemination is the core mission of the European Journal of Taxonomy. In this way, EJT enhances the immediate discoverability and usability of the taxonomic information it publishes, making it more valuable to the scientific community as a whole. Adherence to the Disentis vision marks a crucial step in the liberation and enrichment of knowledge about biodiversity.”

said Laurence Bénichou, founder and liaison officer of the European Journal of Taxonomy.

The Chief Executive Officer of Meise Botanic Garden, Steven Dessein, who attended the Disentis Symposium, commented:

“Meise Botanic Garden fully supports the Disentis Roadmap, which builds on the foundation laid by the Bouchout Declaration. Open biodiversity data is essential to tackling today’s pressing environmental challenges, from biodiversity loss to climate change. By ensuring research publications become more accessible and interconnected, this roadmap represents a critical step toward harnessing biodiversity knowledge for science, policy, and conservation.”

Christophe Déssimoz, Executive Director of the SIB Swiss Institute of Bioinformatics, another signatory of the Disentis Roadmap, added:

“We have long championed the principles of open, structured, and interoperable data to advance life sciences. The Disentis Roadmap applies these same principles to biodiversity knowledge, ensuring that critical data is not just available, but truly actionable for research, policy, and conservation.”

The director of the Botanic Garden and Botanical Museum of Berlin, Thomas Borsch, noted that more than any other branch of science, taxonomic research depended on the machine-actionable availability of biodiversity data from the literature:

“The ‘Libroscope’ postulated in the Disentis Roadmap will enable a new generation of research workflows through its interoperable approach,” said Professor Borsch. “This will be very helpful to address pressing issues in biodiversity research and in particular to improve the use of quality information on organisms in national and global assessments.”

The chief scientist of the national museum of natural history in Paris (MNHN) said:

“We, like all similar museums and taxonomic institutions, are focussed on linking taxonomic and collection data with digital reproductions and molecular information to create the ‘extended digital specimen.’ However, the potential of taxonomic publications and text mining should not be underestimated either. On the contrary, it is a smart and accessible way to dig into scientific publications so as to retrieve, link and consolidate, research data of great relevance to many disciplines. This is why our institution fully supports the Disentis initiative.”

Christos Arvanitidis, CEO of the Biodiversity and Ecosystem e-Science Infrastructure LifeWatch ERIC, commented:

“LifeWatch ERIC is proud to be part of this initiative, as providing access and support to biodiversity and ecosystem data is fully aligned with our mission. The Disentis Roadmap opens up new opportunities for our research infrastructure to help make what science has provided us accessible and usable, and to improve the FAIRness of data for research and science-based policy.”

Tim Robertson, deputy director and head of informatics at the Global Biodiversity Information Facility (GBIF), who also attended the Disentis meeting added:

“We’re excited to see the results from Disentis partners like Plazi, BHL, Pensoft and the European Journal of Taxonomy who are focussed on liberating data connected with scientific publications,” said . “GBIF will continue to do our part to improve the standards, tools and services that help expand both the benefits and the impact of FAIR and open data on biodiversity science and policy.”

Olaf Bánki, Executive Director of the Catalogue of Life, commented:

“We call out to the scientific community, especially the younger generation, to join our effort in unlocking biodiversity data from literature. Actionable biodiversity and taxonomic data from digitized literature contributes to creating an index of all described organisms of all life on earth. We need such data to tackle and understand the current biodiversity crisis.”


Follow the Disentis Roadmap on Bluesky, Mastodon, and LinkedIn.

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.
  • 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.

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:

Pensoft’s statement on the European Union’s Conclusions on OA scholarly publishing

We are firm supporters of healthy competition that drives innovation and revolutionary technologies, while supporting freedom of choice.

On behalf of Pensoft Publishers, we express our support for the Conclusions on high-quality, transparent, open and equitable scholarly publishing, recently published by the Council of the European Union. We do share all concerns articulated in the document that highlight major inequities and outstanding issues in the scholarly publishing environment.

In our opinion, it is of utmost importance to promptly address the existing issues in the publishing system, where healthy competition can thrive and contribute to a reality safe from potential mono-/oligopolies and corporate capture.

We firmly believe that only an industry that leaves room for variously-scaled pioneers and startups is capable of leading a long-awaited shift to a high-quality, transparent, open and equitable scholarly publishing landscape aligning with the principles of FAIRness.

Yet, we shall acknowledge that the industry has so far failed to eradicate the most fundamental flaw of the past. In the beginning, the main aim of the Open Access (OA) movement was removing the barrier to access to publicly funded scientific knowledge and scrapping costly subscription fees.

Recently, however, the industry’s biggest players merely replaced it with a barrier to publication by introducing costly Article Processing Charges (APCs) and “big deals” signed between top commercial publishers and academic institutions or national library consortia. 

As a result, small and middle-sized open-access publishers, which have, ironically, been the ones to lead the change and transition to OA by default and oppose the large commercial publishers’ agenda, were effectively pushed out of the scene. Further, we are currently witnessing a situation where OA funds are mostly going to the ones who used to oppose OA.

So, we strongly support measures that ensure an inclusive and FAIR competition, which could in turn prompt quality, sustainability and reasonable pricing in scholarly publishing. In our opinion, an environment like this would actually foster equality and equity amongst all publishers, either small, large, non-profit, commercial, institutional or society-based. 

One of the main points of the conclusions is a recommendation for a general use of the Diamond OA model, where no charges apply to either researchers or readers. While we fully support the Diamond OA model, we wish to stress on the fact that considerable concerns about the sustainability of existing Diamond OA models remain.

On the one hand, there are OA agreements (also known as read-and-publish, publish-and-read, transformative agreements etc.), typically signed between top publishers and top research institutions/consortia. This OA model is often mistakenly referred to as “Diamond OA”, since authors affiliated with those institutions are not concerned with providing the APC payment – either by paying themselves or applying for funding. Instead, the APCs are paid centrally. Most often, however, journals published by those publishers are still directly charging authors who are not members of the signed institutions with, in our opinion, excessive APCs. Even if those APCs are covered by a signed institution, these are still considerable funds that are being navigated away from actual research work. 

On the other hand, there are independent researchers, in addition to smaller or underfunded institutions, typically – yet far from exclusively – located in the developing world, who are effectively being discriminated against. 

In conclusion, this type of contracts are shutting away smaller actors from across academia just like they used to be under the subscription-based model. Hereby, we wish to express our full agreement with the Council of the European Union’s conclusion, that “it is essential to avoid situations where researchers are limited in their choice of publication channels due to financial capacities rather than quality criteria”.

There are also several alternative OA models designed to lessen the burden of publication costs for both individual researchers, libraries and journal owners. However, each comes with its own drawbacks. Here – we believe – is where the freedom of choice is perhaps most needed, in order to keep researchers’ and publishers’  best interests at heart. 

One of those alternatives is open-source publishing platforms, which – by design – are well-positioned to deliver actual Diamond OA for journals, while maintaining independence from commercial publishers. However, the operational model of this type of publishing and hosting platforms would most often only provide a basic infrastructure for editors to publish and preserve content. As a result, the model might require extra staff and know-how, while remaining prone to human errors. Additionally, a basic technological infrastructure could impede the FAIRness of the published output, which demands advanced and automated workflows to appropriately format, tag semantically and export scientific outputs promptly after publication.

Similarly, large funders and national consortia have put their own admirable efforts to step up and provide another option for authors of research and their institutions. Here, available funds are allocated to in-house Diamond OA publishing platforms that have originally been designed according to the policies and requirements of the respective funding programme or state. However, this type of support – while covering a large group of authors (e.g. based in a certain country, funded under a particular programme, and/or working in a specific research field) – still leaves many behind, including multinational or transdisciplinary teams. Additionally, due to the focus on ‘mass supply’, most of these OA publishing platforms have so far been unable to match their target user base with the appropriate scale of services and support.

What we have devised and developed at Pensoft with the aim to contribute to the pool of available choices is an OA publishing model, whose aim is to balance cost affordability, functionality, reliability, transparency and long-term sustainability. 

To do so, we work with journal owners, institutions and societies to create their own business and operational model for their journals that matches two key demands of the community: (1) free to read and free to publish OA model, and, (2) services and infrastructure suited for Diamond OA at a much lower cost, compared to those offered by major commercial publishers.

In our opinion, independent small publishers differentiate from both large commercial publishers and publicly funded providers by relying to a greater extent on innovative technology and close employee collaboration.

As a result, they are capable of delivering significantly more customisable solutions – including complete packages of automated and human-provided services – and, ultimately, achieving considerably lower-cost publishing solutions. Likewise, they might be better suited to provide much more flexible business models, so that libraries and journal owners can easily support (subsets of or all) authors to the best of their capabilities.

While we realise that there is no faultless way to high-quality, transparent, open and equitable scholarly publishing, we are firm supporters of an environment, where healthy competition prompts the continuous invention and evolution of tools and workflows

Our own motivation to invest in scholarly publishing technology and its continuous refinement and advancement, coupled with a number of in-house and manually provided services, which is reflected in our APC policies, aligns with the Council’s statement that “scientific practices for ensuring reproducibility, transparency, sharing, rigour and collaboration are important means of achieving a publishing system responsive to the challenges of democratic, modern and digitalised societies.”

Our thinking is that – much like in any other industry – what drives innovation and revolutionary technologies is competition. To remain healthy and even self-policing, however, this competition needs to embrace transparency, equity and inclusivity.

Last, but not least, researchers need to have the freedom to choose from plenty of options when deciding where and how to publish their work!

Senckenberg Nature Research Society’s General director Prof. Klement Tockner on a visit at the National Museum of Natural History and Pensoft

An important discussion point was the performance of the four Senckenberg journals, which moved to Pensoft’s publishing platform a few years ago. On the agenda was also the opportunity for an Open Access agreement

Prof. Klement Tockner, Director general of the Senckenberg Society for Nature Research (centre) with Pensoft’s founder and CEO Prof. Lyubomir Penev (right) and Prof. Pavel Stoev, Director of the National Museum of Natural History (Bulgaria) and COO at Pensoft (left).

On 2 June 2023, we welcomed Prof. Klement Tockner, Director general of the Senckenberg Society for Nature Research, who travelled to Bulgaria to meet with Pensoft’s and the National Museum of Natural History’s (NMNHS) senior management to discuss current and future collaborations. 

The visit took place in the NMNHS, where Tockner had fruitful discussions with Pensoft’s founder and CEO Prof. Lyubomir Penev and Prof. Pavel Stoev, Director of the Museum and COO at Pensoft.

An important point in the discussion was the performance of the four scientific journals, owned by the Society, which moved to Pensoft’s publishing platform ARPHA a couple of years ago, and marked the beginning of a fruitful and highly promising partnership.

On the agenda was also the opportunity for an Open Access agreement to be signed between the Society and the publisher, in order to support researchers who wish to publish in any Pensoft journal. 

Tockner was also curious to learn more about the additional publishing services, provided by Pensoft via the ARPHA platform, including the various and continuously elaborated data publishing workflows, and the opportunities to streamline the description of new marine species, identified from DNA material.

In early 2021, the Senckenberg Society for Nature Research signed with the publisher to move three of its legacy titles from the natural sciences domain: Arthropod Systematics & Phylogeny, Contributions to Entomology, Geologica Saxonica and Vertebrate Zoology.

Later the same year, in November, the journal Contributions to Entomology followed suit. All four of them went for the white-label publishing solution available from ARPHA, designed to preserve the exclusive identity of historical journals.

The partners also talked about further extending the collaboration between Senckenberg and Pensoft to European Commission-funded scientific projects. Tockner was particularly fascinated with the progress made by the currently undergoing project Biodiversity Community Integrated Knowledge Library (BiCIKL), coordinated by Pensoft and involving 14 European institutions from ten countries. Additionally, over the past 20 years, Pensoft has also partnered in over 50 different consortia as a publisher, science communicator and technology provider.

Stoev (right) showing Tockner (left) around the collections of the National Museum of Natural History (Sofia, Bulgaria).

In his role as Director of the NMNHS, Stoev used the occasion to tour Tockner around the NMNHS collections and tell him more about the Museum’s latest achievements and projects, as well as its traditions in the fields of human evolution research and paleornithology.

Stoev (left) tells Tockner (right) more about the recently launched Bulgarian national unit of DiSSCo.

The two also engaged in a vivid discussion about the poorly studied biodiversity in Bulgaria and the region, but also about the recent efforts of the NMNHS team, including the launch of a Bulgarian national unit of DiSSCo tasked to digitise a large proportion of the institution’s collection in the next three years. Tockner and Stoev also talked about the need of additional networking activities and closer collaborations between smaller natural history museums across Europe that could be mediated through the Consortium of European Taxonomic Facilities (CETAF), where Senckenberg is an active member.

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Follow ARPHA Platform on Twitter and LinkedIn for further updates.

Eye for Detail: Papers in Pensoft journals sport a new look

As behaviours and needs of readers change, we strive to keep up with the times. Let’s run through what & why has changed to the PDF format.

Readers at some of the journals published by Pensoft, who have downloaded/printed a publication or ordered a physical copy of a journal issue over the last few weeks, might be in for a surprise concerning the layout of the PDF format of the articles. 

Research papers published in ZooKeys demonstrating the former (left) and the current (right) article layout seen in the PDF format. 

Even though it’s been years since online publishing has become the norm in how we are consuming information – including scientific publications – we understand that academia is still very much fond of traditional, often paper-based, article layout format: the one you use when accessing a PDF file or a print copy, rather than directly scrolling down through the HTML version of the article. 

Even if today large orders of printed volumes from overseas are the exception, rather than the rule, we know we have readers of ours who regularly print manuscripts at home or savе them on their devices. Trends like this have already led to many journals first abandoning the physical- for digital-first, then transitioning to digital-only publication format.

Meanwhile, it is true that needs and demands have fundamentally changed in recent times. 

As we speak, readers are accessing PDF files from much higher-quality desktops, in order to skim through as much content as possible. 

In the meantime, authors are relying on greater-quality cameras to document their discoveries, while using advanced computational tools capable of generating and analysing extra layers of precise data. While producing more exhaustive research, however, it is also of key importance that their manuscripts are processed and published as rapidly as possible.

So, let’s run through the updates and give you our reasoning for their added value to readers and authors.

Revised opening page

One of the major changes is the one to the format of the first page. By leaving some blank space on the left, we found a dedicated place for important article metadata, i.e. academic editor, date of manuscript submission / acceptance / publication, citation details and licence. As a result, we “cleaned up” the upper part of the page, so that it can better highlight the authors and their affiliations. 

Bottom line: The new layout provides a better structure to the opening page to let readers find key article metadata at a glance. 

Expand as much – or as little – as comfortable

As you might know, journals published by Pensoft have been coming in different formats and sizes. Now, we have introduced the standard A4 page size, where the text is laid in a single column that has been slightly indented to the right, as seen above. Whenever a figure or a table is used in a manuscript, however, it is expanded onto the whole width of the page.

Before giving our reasons why, let’s see what were the specific problems that we address.

Case study 1

Some of our signature journals, including ZooKeys, PhytoKeys and MycoKeys, have become quite recognisable with their smaller-than-average B5 format, widely appreciated by people who would often be seen carrying around a copy during a conference or an international flight.

However, in recent times, authors began to embrace good practices in research like open sharing of data and code, which resulted in larger and more complex tables. Similarly, their pocket-sized cameras would capture much higher-resolution photos capable of revealing otherwise minute morphological characters. Smaller page size would also mean that often there would be pages between an in-text reference of a figure or a table and the visual itself.

So, here we faced an obvious question: shall we deprive their readers from all those detailed insights into the published studies?

Case study 2

Meanwhile, other journals, such as Herpetozoa, Zoosystematics and Evolution and Deutsche Entomologische Zeitschrift, had long been operating in A4 size, thereby providing their readers with a full view of the figures in their publications. 

Yet, the A4 format brought up another issue: the lines were too long for the eye comfort of their readers. 

What they did was organise their pages into two-column format. While this sounds like a good and quite obvious decision, the format – best known from print newspapers – is pretty inconvenient when accessed digitally. Since the readers would like to zoom in on the PDF page or simply access the article on mobile, they will need to scroll up and down several times per page. 

In addition, the production of a two-column text is technologically more challenging, which results in extra production time.

Bottom line: The new layout allows journals to not sacrifice image quality for text readability and vice versa. As a bonus, authors enjoy faster publication for their papers.

Simplified font

If you have a closer look at the PDF file, you would notice that print-ready papers have also switched to a more simplistic – yet easier to the eye – font. Again, the update corresponds to today’s digital-native user behaviour, where readers often access PDF files from devices of various resolutions and skim through the text, as opposed to studying its content in detail.

In fact, the change is hardly new, since the same font has long been utilised for the webpages (HTML format) of the publications across all journals.

Bottom line: The slightly rounder and simplified font prompts readability, thereby allowing for faster and increased consumption of content. 

What’s the catch? How about characters and APCs?

While we have been receiving a lot of positive feedback from editors, authors and readers, there has been a concern that the updates would increase the publication charges, wherever these are estimated based on page numbers.

Having calculated the lines and characters in the new layout format, we would like to assure you that there is no increase in the numbers of characters or words between the former and current layout formats. In fact, due to the additional number of lines fitting in an A4 page as opposed to B5, authors might be even up for a deal.

________

* At the time of the writing, the new paper layout has not been rolled out at all journals published by Pensoft. However, most of the editorial boards have already confirmed they would like to incorporate the update.

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One Ecosystem selected for inclusion in the Web of Science

“Not only does it mean that content is persistent in merit and quality, but that innovative research outputs are already appreciated within academia,” says Editor-in-Chief Prof Dr Benjamin Burkhard

Seven years after its official launch in May 2016, the One Ecosystem journal has successfully completed the rigorous quality and integrity assessment at Web of Science.

Scientific papers published in One Ecosystem from 2021 onwards will be indexed at the Emerging Sources Citation Index (ESCI) and the Journal Citation Reports (JCR), revealed the Indexing team at ARPHA Platform.

The news means that One Ecosystem might see its very first Journal Impact Factor (JIF) as early as 2024, following the latest revision of the metric’s policies Clarivate announced last July. According to the update, all journals from the Web of Science Core Collection are now featured in the Journal Citation Reports, and thereby eligible for a JIF.

“Giving all quality journals a Journal Impact Factor will provide full transparency to articles and citations that have contributed to impact, and therefore will help them demonstrate their value to the research community. This decision is aligned to our position that publications in all quality journals, not just highly cited journals, should be eligible for inclusion in research assessment exercises,” said back then Dr Nandita Quaderi, Editor-in-Chief and Editorial Vice President at Web of Science.

“We are happy to learn that Web of Science has recognised the value and integrity of One Ecosystem in the scholarly landscape. Not only does it mean that the scientific content One Ecosystem has been publishing over the years is persistent in merit and quality, but that innovative research outputs are already widely accepted and appreciated within academia.

After all, one of the reasons why we launched One Ecosystem and why it has grown to be particularly distinguished in the field of ecology and sustainability is that it provides a scholarly publication venue for traditional research papers, as well as ‘unconventional’ scientific contributions,”

comments Prof Dr Benjamin Burkhard, Executive Director at the Institute of Physical Geography & Landscape EcologyLeibniz University Hannover (Germany) and founding Editor-in-Chief of One Ecosystem.

“These ‘unconventional’ research outputs – like software descriptions, ecosystem inventories, ecosystem service mappings and monitoring schema – do not normally see the light of day, let alone the formal publication and efficient visibility. We believe that these outputs can be very useful to researchers, as well as practitioners and public bodies in charge of, for example, setting up indicator frameworks for environmental reporting,”

says Prof Davide Geneletti, Department of Civil, Environmental and Mechanical Engineering of University of Trento, Italy, and Deputy Editor-in-Chief of One Ecosystem.

“In fact, last year, we also launched a new article type: the Ecosystem Accounting table, which follows the standards set by the the System of Environmental-Economic Accounting Ecosystem Accounting (SEEA EA). This publication type provides scientists and statisticians with a platform to publish newly compiled accounting tables,” 

adds Dr Joachim Maes, Policy analyst at the Directorate-General for Regional and Urban Policy of the European Commission and Deputy Editor-in-Chief of One Ecosystem.

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Previously, One Ecosystem has been accepted for indexing at over 60 major academic databases, including ScopusDOAJCabell’s DirectoryCABI and ERIH PLUS. In June 2022, the journal received a Scopus CiteScore reading 7.0, which placed it in Q1 in five categories: Earth and Planetary Sciences; Ecology; Nature and Landscape Conservation; Agricultural and Biological Sciences (miscellaneous); Ecology, Evolution, Behavior and Systematics.

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You can follow One Ecosystem on Twitter and Facebook.