Tag: journals

Smithsonian’s Dr Torsten Dikow appointed Editor-in-Chief of ZooKeys

Dikow, an esteemed entomologist specialising in Diptera and cybertaxonomy, is the new Editor-in-Chief of the leading scholarly journal in systematic zoology and biodiversity

Esteemed entomologist specialising in true flies (order Diptera) and cybertaxonomy, Dr Torsten Dikow was appointed as the new Editor-in-Chief of the leading open-access peer-reviewed journal in systematic zoology and biodiversity ZooKeys.

Dikow is to step into the shoes of globally celebrated fellow entomologist and colleague at the Smithsonian and founding Editor-in-Chief of ZooKeys Dr Terry Erwin, who sadly passed away in May, 2020, leaving behind hefty scientific legacy and immeasurable admiration and fond memories. 

Today, Dikow is a Research Entomologist and Curator of Diptera and Aquatic Insects at the Smithsonian National Museum of Natural History (Washington, DC, USA), where his research interests encompass the diversity and evolutionary history of the superfamily Asiloidea – or asiloid flies – comprising curious insect groups, such as the assassin flies / robber flies and the mydas flies. Amongst an extensive list of research publications, Dikow’s studies on the diversity, biology, distribution and systematics of asiloid flies include the description of 60 species of assassin flies alone, and the redescription of even more through comprehensive taxonomic revisions.

Dikow obtained his M.S. in Zoology from the Universität Rostock (Germany) and Ph.D. in Entomology from Cornell University (New York, USA) with three years of dissertation research conducted at the American Museum of Natural History (AMNH). 

During his years as a postdoc at the Field Museum (Illinois, USA), Dikow was earnestly involved in the broader activities of the Encyclopedia of Life through its Biodiversity Synthesis Center (BioSynC) and the Biodiversity Heritage Library (BHL). There, he would personally establish contacts with smaller natural history museums and scientific societies, and encourage them to grant digitisation permissions to the BHL for in-copyright scientific publications. Dikow is a champion of cybertaxonomic tools and making biodiversity data accessible from both natural history collections and publications. He has been named a Biodiversity Open Data Ambassador by the Global Biodiversity Information Facility (GBIF).

Dikow is no stranger to ZooKeys and other journals published by the open-access scientific publisher and technology provider Pensoft. For the past 10 years, he has been amongst the most active editors and a regular author and reviewer at ZooKeys, Biodiversity Data Journal and African Invertebrates.

“Publishing taxonomic revisions and species descriptions in an open-access, innovative journal to make data digitally accessible is one way we taxonomists can and need to add to the biodiversity knowledge base. ZooKeys has been a journal in support of this goal since day one. I am excited to lend my expertise and enthusiasm to further this goal and continue the development to publish foundational biodiversity research, species discoveries, and much more in the zoological field,”

said Dikow.

Dikow took on his new role at ZooKeys at a time when the journal had just turned 15 years on the scholarly publishing scene. In late 2020, the scientific outlet also marked the publication of its 1000th journal volume.

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Visit the journal’s website and follow ZooKeys on X (formerly Twitter) and Facebook. You can also follow Torsten Dikow on X.

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About ZooKeys:

ZooKeys is a peer-reviewed, open-access, rapidly disseminated journal launched to accelerate research and free information exchange in taxonomy, phylogeny, biogeography and evolution of animals. ZooKeys aims to apply the latest trends and methodologies in publishing and preservation of digital materials to meet the highest possible standards of the cybertaxonomy era.

ZooKeys publishes papers in systematic zoology containing taxonomic/faunistic data on any taxon of any geological age from any part of the world with no limit to manuscript size. To respond to the current trends in linking biodiversity information and synthesising the knowledge through technology advancements, ZooKeys also publishes papers across other taxon-based disciplines, such as ecology, molecular biology, genomics, evolutionary biology, palaeontology, behavioural science, bioinformatics, etc. 

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.

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Nanopublications tailored to biodiversity data

Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.

First off, why nanopublications?

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability. 

By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data. 

With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable manner in line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.

The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards. 

Now, what’s new?

As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:

  1. Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
  1. Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
  1. Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).

Nanopublications for biodiversity data?

At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proof the most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments. 

On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.

Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:

So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences. 

Nanopublication template customised for biodiversity research publications available from Nanodash.

As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks. 

The novel domain-specific publication format was launched as part of the collaboration between Knowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisher Pensoft.

… so, what exactly is a nanopublication?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained on nanopub.net.

Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.

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

In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs. 

“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”

said Prof. Lyubomir Penev, founder and CEO at Pensoft, which had published the very first semantically enhanced research article in the biodiversity domain back in 2010 in the ZooKeys journal.

Why are nanopublications necessary?

By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragments of scientific information is interconnected and traceable back to its author(s) and scientific evidence. 

A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels. 

By building on shared knowledge representation models, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts. 

Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.

A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way. 

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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal. 

Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!

This Nanopublications for biodiversity workflow was created with a partial support of the European Union’s Horizon 2020 BiCIKL project under grant agreement No 101007492 and in collaboration with Knowledge Pixels AG.The tool uses data and API services of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, Environmental Ontology (ENVO), Relation Ontology (RO), NOMEN, ZooBank, Index Fungorum, MycoBank, IPNI, TreatmentBank, and other resources. 

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On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.

Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.

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How it works: Nanopublications linked to articles in RIO Journal

Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.

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!

Beware of scientific scams! Tips to avoid predatory publishing in biological journals

Predatory publishing has been growing exponentially, with severe consequences for society and the environment.

Guest blog post by Cássio Cardoso Pereira, Gabriela França Fernandes, and Walisson Kenedy Siqueira

We are bombarded day and night with slot-machine invitations from journals, books, and events such as congresses and lectures. Predatory publishing has reached alarming levels in biology, which is why we published an editorial in the journal Neotropical Biology and Conservation to alert the community, show the modus operandi of these publishers, and pass on good practices so that researchers, especially beginners, can escape this trap.

Piggybacking on the open access movement, numerous predatory publishers have emerged in search of easy profits. These cybercriminals take advantage of the publish-or-perish culture without providing any information about their peer-review protocols, concerned not with the scientific, bibliographic, or ethical aspects of publishing, but with the money received from authors.

The number of predatory publishers has grown exponentially in recent years and spread across all areas of knowledge, including biology. It is a common practice of these journals, often with an equally fake editorial staff, to send electronic invitations to potential authors to publish articles. These invitations are often facilitated by initial screenings of the emails of corresponding authors available on the internet. The emailed invitations from the supposed editors often stress that the author’s work is sound and, since it has already gone through the scrutiny of the editorial board, requires only the payment of a fee to publish it, with no need for further peer review.

Invitations to join the editorial board of these journals are also frequent, mostly intended to take advantage of the scientists’ prestige. Instead of editing articles, these invited editors are used as poster boys, i.e., they have their names published on the journal’s website, thus attracting unsuspecting authors to submit their manuscripts.

These journals are generally not included in the directory of open access journals (DOAJ) and are not indexed in the main bibliometric databases, such as Google Scholar, SciELO, Scopus, and Web of Science, for the simple reason that they do not meet their inclusion criteria. The websites of these journals often have little information about the editorial board, have a fake International Standard Serial Number (ISSN), lack transparency regarding their scope, provide no indication of a policy of retraction, have no transparency regarding copyright transfer, and provide very vague contact information, often omitting the address of the journal’s office.

In addition to papers, there are also invitations to publish books and book chapters with fake International Standard Book Numbers and dubious editorial boards. There is also a flood of invitations to predatory meetings, such as online conferences, symposia, workshops, and lectures. These often have websites that are equally confusing and never linked to a university or a postgraduate program. Above all, one should consult advisors, supervisors, or senior colleagues about the invitation and the sender’s academic reputation. In any case, one must pay attention not only to the citation metrics but also, mainly, to their editorial board, ISSN, ISBN, contact information, and relationships with recognized institutions.

When we analyze the impacts of predatory publishing on the scientific community, the worst problems are:

  • the dissemination of erroneous information about scientific problems of interest
  • the facilitation of plagiarism
  • the waste of public resources intended for publication
  • the appointment of researchers at universities and research institutes based on curricula full of doubtful publications, generating negative cascading effects that undermine higher education as a whole.

The damage done to society can be even worse. Governments, large companies, and decision-makers can be misled by false information, resulting in attitudes that undermine responses to major human problems such as climate change, biodiversity, and pandemics.

Efforts to fight predatory publishers require collaboration and support at higher levels. Governments need to create regulatory agencies that carefully and systematically evaluate the activities carried out by scientific journals. Science funding agencies should require that publication fees be paid only to publishers that adhere to an internationally recognized set of transparency and ethical rules. We need to discuss our values and incentives in the academic community, so we can start prioritizing quality over quantity. This would provide a reference point for research, help design coherent interventions, and improve information and public policy in favor of society and the environment.

Reference:

Pereira CC, Mello MAR, Negreiros D, Figueiredo JCG, Kenedy-Siqueira W, Maia LR, Fernandes S, Fernandes GFC, Ponce de Leon A, Ashworth L, Oki Y, de Castro GC, Aguilar R, Fearnside PM, Fernandes GW (2023) Beware of scientific scams! Hints to avoid predatory publishing in biological journals. Neotropical Biology and Conservation 18(2): 97-105. https://doi.org/10.3897/neotropical.18.e108887

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 Ecology, Leibniz 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 Scopus, DOAJ, Cabell’s Directory, CABI 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.

Pensoft’s ARPHA Publishing Platform integrates with OA Switchboard to streamline reporting to funders of open research

By the time authors open their inboxes to the message their work is online, a similar notification will have also reached their research funder.

Image credit: OA Switchboard.

By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.

This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.

All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.

“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”

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

 

“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”

adds Yvonne Campfens, Executive Director of the OA Switchboard.

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About the OA Switchboard:

A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.

About Pensoft:

Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.

All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.

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Follow OA Switchboard on Twitter and Linkedin.

Fossil Record, a Natural History Museum of Berlin journal moves to ARPHA

Having been publishing its historically renowned Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution in partnership with Pensoft since 2014, the Museum extends the collaboration by moving a third signature journal

Having been publishing its historically renowned scientific journals Deutsche Entomologische Zeitschrift (DEZ) and Zoosystematics and Evolution (ZSE) in partnership with the scholarly publisher Pensoft and its ARPHA Platform since 2014, the Natural History Museum of Berlin (Museum für Naturkunde Berlin) now extends the collaboration by moving a third signature journal: Fossil Record. 

Launched in 1998 under the name Mitteilungen aus dem Museum für Naturkunde Berlin, Geowissenschaftliche Reihe, Fossil Record is the Natural History Museum of Berlin’s palaeontological journal. Published in two issues a year, the open-access scientific outlet covers research from all areas of palaeontology, including the taxonomy and systematics of fossil organisms, biostratigraphy, palaeoecology, and evolution. It deals with all taxonomic groups, including invertebrates, microfossils, plants, and vertebrates.

Following its move to ARPHA, Fossil Record is to utilise the whole package of ARPHA Platform’s services, including its fast-track, end-to-end publishing module, designed to appeal to readers, authors, reviewers and editors alike. 

With ARPHA, each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving the platform’s collaboration-centred online environment. The articles are made available in PDF and machine-readable JATS XML formats, as well as semantically enriched HTML for better and mobile-friendly reader experience. 

As a result, the journal’s articles are as easy to discover, access, reuse and cite as possible. Once published, the content is indexed and archived instantaneously and its underlying data exported to relevant specialised databases. Simultaneously, a suite of various metrics is enabled to facilitate tracking the usage of articles and sub-article elements, such as figures and tables.

“We have deeply enjoyed our collaboration with the Natural History Museum of Berlin for the past seven years that started with two great journals moving to our scholarly portfolio and advanced open access. Now, I am delighted to strengthen this wonderful partnership by welcoming Fossil Record and its fantastic editorial team to the families of ARPHA and Pensoft. I am certain that together we will not only repeat the success we had with DEZ and ZSE, but will actually build on it,”

says Prof. Dr Lyubomir Penev, founder and CEO at ARPHA and Pensoft.

About the Natural History Museum of Berlin:

The “Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science” is an integrated research museum within the Leibniz Association. It is one of the most important research institutions worldwide in the areas of biological and geological evolution and biodiversity.

The Museum’s mission is to discover and describe life and earth – with people, through dialogue. As an excellent research museum and innovative communication platform, it wants to engage with and influence the scientific and societal discourse about the future of our planet, worldwide. Its vision, strategy and structure make the museum an excellent research museum. The Natural History Museum of Berlin has research partners in Berlin, Germany and approximately 60 other countries. Over 700,000 visitors per year as well as steadily increasing participation in educational and other events show that the Museum has become an innovative communication centre that helps shape the scientific and social dialogue about the future of our earth.

Seven journals moving to ARPHA in early 2020 showcase the versatility of the publishing platform

Seven journals of diverse backgrounds, scopes and geographies are moving to Pensoft-developed open access publishing platform ARPHA.

A full-featured, open access publishing platform for journals, books and data, which comes with an extensive list of services and features – both automated and human-provided – to adapt to the individual needs of any client journal. But how does that translate into practice? 

The latest scholarly titles to join the ranks of ARPHA might just provide a perfect example of the capabilities of the platform to accommodate the specificity of scholarly journal across sciences, audiences, geographies and languages.

Amsterdam University Press strengthens partnership with ARPHA by launching two brand new journals

Journal of European Landscapes (JEL) and Heritage, Memory and Conflict Journal (HMC) add up to the partnership between ARPHA and Amsterdam University Press (AUP), which started in early 2018 with the transfer of the only Dutch-language open-access journal focussing on accountancy, business economics and related areas: Accountancy and Business Economics, or Maandblad voor Accountancy en Bedrijfseconomi (MAB).

Homepage of Amsterdam University’s journal Accountancy and Business Economics (Maandblad voor Accountancy en Bedrijfseconomi), using the white-label publishing solution of ARPHA Platform.

Not only was MAB the first journal on the platform that publishes articles exclusively in a language other than English, but also became an impressive precedent with its nearly 100-year content that got successfully dusted off and fitted into the user-friendly digital environment of today. All papers ever issued in MAB since its launch in 1923, were re-published, so that each could be assigned with a DOI; have its metadata registered on CrossRef; and its article content fully searchable within the PDF copy.

All three make use of ARPHA’s white-label publishing solution, which allows for AUP to carry its recognisable logo through a unified banner across the websites of the journals. Unlike MAB, however, JEL and HMC are to have their articles published exclusively in English to further promote their international scope and focus.

Heritage, Memory and Conflict Journal (HMC)

Homepage of the new Heritage, Memory and Conflict Journalpublished by Amsterdam University Press via ARPHA Platform.

Heritage, Memory and Conflict Journal is a brand new journal launched to trace back the remnants of the past – be it physical or anecdotal – back to their roots in the days of old. How do memory sites and discourses operate as vehicles at local, national and transnational levels and what indeed is the ‘cargo’ they carry? This is the type of questions authors from across disciplines – academic, artistic and industrial – will be trying to answer when preparing their manuscripts for HMC. 

Journal of European Landscapes (JEL) 

Homepage of the new Journal of European Landscapes published by Amsterdam University Press via ARPHA Platform.

Similarly, the second newly launched Journal of European Landscapes is to turn to history and cultural heritage, in order to understand the present use of the past when it comes to landscape. JEL’s founders point out that while Europe’s landscapes have so far enjoyed quite a lot of scientific attention, there isn’t a journal to address its indisputable and critical connection to heritage, even though the latter is what connects historical research with modern planning and management.

Vegetation Classification and Survey (VCS)

Homepage of the new Vegetation Classification and Survey journal published by the International Association for Vegetation Science via ARPHA Platform.

Adding up to the landscape topic is the Vegetation Classification and Survey (VCS) journal. This is the latest outlet launched by the International Association for Vegetation Science (IAVS): a worldwide union of scientists and other aficionados of theory and practice concerning the study of vegetation. 

With its transfer to ARPHA, VCS fulfils the mission of the union to move to Open Access. Interestingly, the journal supports two permanent sections: Ecoinformatics and Phytosociological Nomenclature. There, authors can submit certain unique article types: Review and Synthesis and Short/Long Database Reports. 

Devoted to plant community ecology, VCS publishes original research that works toward the development of novel vegetation classifications, as well as applied studies that use such typologies. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping. 

Plant Sociology 

Homepage of the new Plant Sociology journal published by Società Italiana di Scienza della Vegetazione via ARPHA Platform.

Another modern botany journal still awaiting its first issue since its transfer to ARPHA, is Plant Sociology, brought to life by the “Società Italiana di Scienza della Vegetazione” (SISV) with the aim to succeed the historical journals of the society: Fitosociologia (1990-2011) and Notiziario della Società Italiana di Fitosociologia (1964-1989).

The editorial management opted to have the journal co-published with Pensoft: the academic publisher and technology provider standing behind ARPHA. Thus, by default, the journal receives some extra perks as a result of Pensoft’s partnerships with leading innovators in the scholarly communication domain.  An excellent example would be the indexing and addition of each Plant Sociology article by the research discovery platform ScienceOpen in the “Pensoft Biodiversity” collection, following a recent strategic collaboration between the two Open Science champions.

With a wide scope covering vegetation studies from plant community to landscape level, Plant Sociology puts a special focus on topics such as plant sociology and vegetation survey for developing ecological models, as well as plant classification, monitoring, assessment, management and conservation, as long as the studies are based on rigorous and quantitative measures of physical and biological components.

Caucasiana

Adding up to the well-pronounced biodiversity theme in ARPHA’s and Pensoft’s journal portfolios, as well as the “Pensoft Biodiversity” collection on ScienceOpen, is the first Georgian journal to join the lines of the publishing platform. Caucasiana is to be co-published by the top biodiversity research centre in the region: Ilia State University in Tbilisi and Pensoft.

The scholarly outlet that we’ll soon see on ARPHA Platform is in fact a successor of an earlier journal launched by the Institute of Zoology of the Georgian Academy of Science that has been revamped top-to-bottom. Transformed into a technologically advanced publishing venue, Caucasiana’s task is to handle the growing research interest in the incredible, yet surprisingly overlooked animal, plant and fungal life of Caucasus and adjacent regions. 

Research published in Caucasiana will be well-positioned to bring this hotspot of biodiversity and endemism into focus for the global conservation movement.

The EASE Journal: European Science Editing (ESE)

The quarterly journal of the European Association of Science Editors (EASE): European Science Editing (ESE) is a key news source for all actors involved in scholarly publishing.

For the first time, ESE will open up its content to the public from day one of its publication, thanks to its move to ARPHA. While digital and print subscriptions used to be included as part of the association’s membership packages, other readers would have had to wait six months after print publication to receive free access.

Launched in 2003, ESE’s aim has been to keep editors posted about everything they need to know concerning scholarly communication. To do so, the journal publishes research articles, meeting reports, essays and viewpoints, as well as book and website reviews. Especially for members of the association, ESE takes care to highlight upcoming events and provide resources and publications, considered to be of their interest. 

Bulgarian Journal of Cardiology

In 2020, ARPHA will also welcome the third Bulgarian-born academic journal and the fourth covering the field of Medical Sciences to its open-access portfolio: the journal of Bulgaria’s National Cardiac Society, which is part of the European Society of Cardiology (ESC).

For the first time, the Bulgarian Journal of Cardiology will make use of the soon-to-be-released English-Bulgarian bilingual publishing solution from ARPHA. Similarly to the English-Russian approach to journal publishing, which was presented in Moscow in early December, ARPHA will allow for users of the Bulgarian Journal of Cardiology to not only publish papers in both English and Bulgarian, but also enjoy a top-to-bottom Bulgarian user interface.

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Learn more about ARPHA’s key features and achievements from 2019 in our yearly recap.