It all began with an opening ceremony complete with live music and stunning visuals, which set the stage for five days of research exchange and collaboration.
Pensoft welcomed faces new and old at a decorated stand featuring numerous illustrated materials designed by scientific illustrator Denitsa Peneva. Manning the stand were Prof Dr Lyubomir Penev (MycoKeys Founding Editor & Pensoft Founder and CEO) and Slavena Peneva (Pensoft Head of Graphic Design).
MycoKeys materials esigned by Denitsa Peneva.Urmas Kõljalg and Lyubomir Penev.Lyubomir Penev, Dmitry Schigel and Slavena Peneva.
The booth hosted a special gathering for MycoKeys editors, including Editor-in-Chief Prof Dr Thorsten Lumbsch, who were shown a video looking back on the history of the journal. Many long-time collaborators of Pensoft, such as Prof Dr Urmas Kõljalg of Pluto F and Dr Dmitry Schigel of Pluto F, also dropped by to say hello.
📢Shoutout to everyone at @IMC12NL who visited our #IMC12 stand AND anyone who has submitted a manuscript to #MycoKeys, reviewed / edited; or simply remembers reading a good paper at our #journal!🍄
The congress provided the perfect opportunity to announce Pensoft’s new, exciting partnership with the International Mycological Association. This collaboration will see the IMAFungus journal move to the ARPHA platform, where it will benefit from cutting-edge publishing technology and workflows.
🔥LIVE from @IMC12NL: one of our most prolific editors & authors: Henrik R. Nilsson, @goteborgsuni with a talk on 'dark' #fungi and the proposal to name #fungi from #DNA#sequences as types.
The next International Mycology Congress will be held in Incheon, South Korea, in 2027. IMC13 already has an active website and the Pensoft team look forward to another exciting installment!
Towards the end of July 2024, members of the Pensoft team travelled to Madrid for the XX International Botanical Congress, where an estimated 3,000 botanists gathered for the biggest event of the year.
Held once every six years, the congress has enlarged its scope over more than a century to become an integrated forum for knowledge on the plant and mycological world.
Proceedings kicked off with a fantastic lecture from PhytoKeys Editor-in-Chief Sandy Knapp titled, “Why botany? Why now?” The following day, Thorsten Lumbsch, Editor-in-Chief of MycoKeys, gave a keynote lecture titled, “Unravelling diversity and evolution of lichens in the genomic era.”
In fact, many authors, editors and readers of Pensoft’s journals were in attendance. And several gave presentations, including a plenary talk by renowned PhytoKeys editor, Pamela S. Soltis, on the changing face of herbarium collections.
Denitsa Peneva greeting researchers at the Pensoft stand.Lyubomir Penev giving a presentation to PhytoKeys editor.
The Pensoft team welcomed attendees with a bespoke stand, complete with print copies, illustrations and various promotional materials depicting beautiful species featured in PhytoKeys.
Lyubomir Penev, founder of Pensoft and founding editor of PhytoKeys, hosted a gathering of PhytoKeys editors at the stand, where he presented the story, latest results and highlights of the journal.
Researchers who found their publications on display at the Pensoft stand.
The congress included numerous lectures, symposia sessions, workshops and meetings across a variety of subject matters, all of which can be found on the IBC 2024 website. The major topics of the event were:
Systematics, phylogenetics, biogeography and evolution
Ecology, environment and global change, including invasive species and plant-animal interactions
Biodiversity and conservation
Structure, physiology and development, including Evo-Devo
Genetics, genomics and bioinformatics
Plants and Society
At the closing ceremony, multiple awards were presented, including Pensoft’s Early Career Researcher Talk Award. Sandy Knapp presented the award to Sonia Molino for her talk on a global study of the genus Parablechnum, a lineage of ferns of the family Blechnaceae. The award grants her a free publication in PhytoKeys.
What a way to end @ibc2024 ! I can't believe how lucky I was to get the Early career researcher talk award on taxonomy or systematics by @Pensoft for my talk at the conference. And delivered by my admired @SandyKnapp! Thank you so much! See you in Cape Town! pic.twitter.com/Y79U1xcKxj
Describing her study, Sofia Molino said: “To date there has been no study that takes into account all the centres of diversity of the genus at the same time, and what we have found is that it has a very complex evolutionary history, with several cases of cryptic diversity, hybridisation and rapid radiation.”
On her plans to use her free publication for a pending study on a series of novelties within Parablechnum in Bolivia, she added: “Although this is probably the country in South America where Parablechnum has been studied the most, after one expedition we have still found a lot of new things, such as several undescribed species, hybrids and new localities of some species that were only known from type material.”
The next International Botanical Congress is in 2029 and will take place in South Africa, where the Pensoft team looks forward to seeing plenty of new faces and old friends!
October and November 2023 were active months for the Pensoft team, who represented the publisher’s journals and projects at conferences in Europe, North America, South America, Oceania and Asia.
Let’s take a look back at all the events of the past two months.
The Biodiversity Information Standards Conference 2023
The annual gathering is a crucial platform for sharing insights, innovations, and knowledge related to biodiversity data standards and practices. Key figures from Pensoft took part in the event, presenting new ways to improve the management, accessibility, and usability of biodiversity data.
Prof. Lyubomir Penev, founder and Chief Executive Officer of Pensoft, gave two talks that highlighted the importance of data publishing. His presentation on “The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data” underscored the significance of FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. BKH is the major output from the Horizon 2020 project BiCIKL (Biodiversity Community Integrated Knowledge Library) dedicated to linked and FAIR data in biodiversity, and coordinated by Pensoft.
Prof. Lyubomir Penev, Pensoft founder and CEO.
He also introduced the Nanopublications for Biodiversity workflow and format: a promising new tool developed by Knowledge Pixels and Pensoft to communicate key scientific statements in a way that is human-readable, machine-actionable, and in line with FAIR principles. Earlier this year, Biodiversity Data Journal integrated nanopublications into its workflow to allow authors to share their findings even more efficiently.
Chief Technology Officer of Pensoft Teodor Georgiev contributed to the conference by presenting “OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph.” His session highlighted the innovative approaches being taken to explore and leverage a biodiversity knowledge graph, showcasing the importance of technology in advancing biodiversity research.
Metabarcoding and Metagenomics editor-in-chief, Florian Leese.
The theme of the conference was “Monitoring Biodiversity for Action” and there was particular emphasis on the development of best practices and new technologies for biodiversity observations and monitoring to support transformative policy and conservation action.
Metabarcoding & Metagenomics’ editor-in-chief, Florian Leese, was one of the organisers of the “Standardized eDNA-Based Biodiversity Monitoring to Inform Environmental Stewardship Programs” session. Furthermore, the journal was represented at Pensoft’s exhibition booth, where conference participants were able to discuss metabarcoding and metagenomics research.
#geobonconf2023 was great as it linked different actors performing #biodiversity monitoring. Today we discussed #eDNA standardisation. We need formal standards, QA/QC, guidance, 🌐harmonisation to facilitate uptake. Cool to see our @DNAquaNet practical guide in this context. pic.twitter.com/eTOtr3yug8
Following the conference, Metabarcoding & Metagenomics announced a new special issue titled “Towards Standardized Molecular Biodiversity Monitoring.” The special issue is accepting submissions until 15th March 2024.
Asian Mycological Congress2023
The Asian Mycological Congress welcomed researchers from around the world to Busan, Republic of Korea, for an exploration of all things fungi from 10-13 October.
MycoKeys Best Talk award (winner not pictured).
Titled “Fungal World and Its Bioexploitation – in all areas of basic and applied mycology,” the conference covered a range of topics related to all theoretical and practical aspects of mycology. There was a particular emphasis on the development of mycology through various activities associated with mycological education, training, research, and service in countries and regions within Asia.
As one of the sponsors of the congress, Pensoft proudly presented a Best Talk award to Dr Sinang Hongsanan of Chiang Mai University, Thailand. The award entitles the winner to a free publication in Pensoft’s flagship mycology journal, MycoKeys.
Joint ESENIAS and DIAS Scientific Conference 2023
The ESENIAS and DIAS conference took place from 11-14 October and focused on “globalisation and invasive alien species in the Black Sea and Mediterranean regions.” Pensoft shared information on their NeoBiota journal and the important REST-COAST and B-Cubed projects.
Polina Nikova receiving the NeoBiota Best Talk Award.
Polina Nikova of the Bulgarian Academy of Sciences received the NeoBiota Best Talk Award for her presentation titled “First documented records in the wild of American mink (Neogale vision von Schreber, 1776) in Bulgaria.” The award entitles her to a free publication in the NeoBiota journal.
XII European Congress of Entomology
Pensoft took part in the XII European Congress of Entomology (ECE 2023) in Heraklion, Crete, from 16-20 October. The event provided a forum for entomologists from all over the world, bringing together over 900 scientists from 60 countries.
Carla Stoyanova, Teodor Metodiev and Boriana Ovcharova representing Pensoft.
The ECE 2023, organised by the Hellenic Entomological Society, addressed the pressing challenges facing entomology, including climate change, vector-borne diseases, biodiversity loss, and the need to sustainably feed a growing world population. The program featured symposia, lectures, poster sessions, and other types of activities aimed at fostering innovation in entomology. For Pensoft, they were a great opportunity to interact with scientists and share their commitment to advancing entomological research and addressing the critical challenges in the field.
🐝Today at #ECE2023, Prof Denis Michez & Sara Reverté are running a workshop on bee identification!
Throughout the event, conference participants could find Pensoft’s team at thir booth, and learn more about the scholarly publisher’s open-access journals in entomology. In addition, the Pensoft team presented the latest outcomes from the Horizon 2020 projects B-GOOD, Safeguard, and PoshBee, where the publisher takes care of science communication and dissemination as a partner.
Group photo of XIV International Congress of Orthopterology 2023 participants.
Hosted for the first time in Mexico, it attracted experts and enthusiasts from around the world. The congress featured plenary speakers who presented cutting-edge research and insights on various aspects of grasshoppers, crickets, and related insects.
Pensoft’s Journal of Orthoptera Research was represented by Tony Robillard, the editor-in-chief, who presented the latest developments of the journal to attendees.
Symposia, workshops, and meetings facilitated discussions on topics like climate change impacts, conservation, and management of Orthoptera. The event also included introductions to new digital and geospatial tools for Orthoptera research.
The 16th International Conference on Ecology and Management of Alien Plant Invasions
4th International ESP Latin America and Caribbean Conference
The 4th International ESP Latin America and Caribbean Conference (ESP LAC 2023) was held in La Serena, Chile, from 6-10 November. Focused on “Sharing knowledge about ecosystem services and natural capital to build a sustainable future,” the event attracted experts in ecosystem services, particularly from Latin America and the Caribbean.
🤩 So excited to be part of the 4th International ESP Latin America and Caribbean Conference, which opens later today! In a great tradition with the ESP conferences, we are offering three full APC waivers for the three best posters.@ESPartnershiphttps://t.co/O97nwEGnMj
Organised by the Ecosystem Services Partnership, this bi-annual conference was open to both ESP members and non-members, featuring a hybrid format in English and Spanish. Attendees enjoyed an excursion to La Serena’s historical center, adding a cultural dimension to the event.
The conference included diverse sessions and a special recognition by Pensoft’s One Ecosystem journal, which awarded full waivers for publication to the authors of the three best posters.
Magaly Aldave receiving the Best Poster Award.
Magaly Aldave of the Transdisciplinary Center for FES-Systemic Studies claimed first prize with “The voice of children in the conservation of the urban wetland and Ramsar Site Pantanos de Villa in Metropolitan Lima, Peru.” Ana Catalina Copier Guerrero and Gabriela Mallea-Rebolledo, both of the University of Chile, were awarded second and third prize respectively.
The event featured in-person and online participation, catering to a wide audience of researchers, academics, and students. It included workshops, presentations, and discussions, with a focus on enhancing understanding in biosystematics.
Pensoft awarded three student prizes at the event. Putter Tiatragu, Australian National University, received the Best Student Talk award and a free publication in any Pensoft journal for “A big burst of blindsnakes: Phylogenomics and historical biogeography of Australia’s most species-rich snake genus.”
Helen Armstrong, Murdoch University, received the Best Student Lightning Talk for “An enigmatic snapper parasite (Trematoda: Cryptogonimidae) found in an unexpected host.” Patricia Chan, University of Wisconsin-Madison, was the Best Student Lightning Talk runner-up for “Drivers of Diversity of Darwinia’s Common Scents and Inflorescences with Style: Phylogenomics, Pollination Biology, and Floral Chemical Ecology of Western Australian Darwinia (Myrtaceae).”
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As we approach the end of 2023, Pensoft looks back on its most prolific and meaningful year of conferences and events. Thank you to everyone who contributed to or engaged with Pensoft’s open-access journals, and here’s to another year of attending events, rewarding important research, and connecting with the scientific community.
For the Pensoft team, September 2023 was a busy and exciting month filled with conferences. Travelling across Europe, they promoted journals, connected with the scientific community, and rewarded exceptional research with free article publications.
Let’s take a look back at all the events of the past month.
Pensoft representatives Mrs. Boriana Ovcharova and Mrs. Anna Sapundzhieva, ready to greet attendees in the sun.
The conference looked at evolutionary adaptations from the perspective of behavioural ecology, reproduction biology, genetics, physiology, as well as nature conservation. It particularly focused on the pressing issues of wildlife research and species conservation in the context of global environmental change. Most of the ≈100 participants were young scientists from more than 30 countries.
The Pensoft team greeted fellow attendees with an exhibition stand and presented the conservation and ecology-focused journals Neobiota, Nature Conservation, One Ecosystem, and Biodiversity Data Journal. Pensoft also advocated for EuropaBon, who are designing an EU-wide framework for monitoring biodiversity and ecosystem services, and REST-COAST, whose mission is to provide the tools to restore environmental degradation of rivers and coasts. Within both European-funded initiatives, Pensoft is a key dissemination partner that contributes expertise in science communication, scholarly publishing, and the development of digital tools and platforms.
Joao Pedro Meireles posing with his Best Poster award.
Pensoft presented Joao Pedro Meireles from Utrecht University with the Best Poster Award for his research on pair compatibility in okapis, entitling him to a free publication in one of Pensoft’s open-access journals.
“My study looked at pair compatibility in the zoo breeding programme of Okapi. During breeding introductions, sometimes the male becomes aggressive towards the female and we decided to investigate the potential factors. We ran a survey among all zoos that house the species in Europe and we found that differences in husbandry were linked to the aggressiveness performed by the males.”
Joao Pedro Meireles, Utrecht University
GfÖ Annual Meeting 2023
From the 12th to 16th of September, the German Centre for Integrative Biodiversity Research hosted the 52nd Annual Meeting of the Ecological Society of Germany, Austria and Switzerlandin Leipzig, Germany. The meeting welcomed more than 1,100 participants from around the world, including scientists, policymakers, educators, and environmental enthusiasts.
This year’s meeting was held with the theme: “The future of biodiversity – overcoming barriers of taxa, realms and scales.” There was a particular emphasis on future challenges and opportunities facing biodiversity, and how to address and manage these in an interdisciplinary and integrative way.
Mrs. Boriana Ovcharova (Pensoft) with Neobiota Editor-in-Chief Prof. Dr. Ingolf Kühn.
Conference participants were welcomed at the Pensoft stand, where they could learn more about the projects EuropaBon and SELINA, which deal with biodiversity, ecosystem and natural capital topics.
Also in Leipzig, the European Conference on Ecological Modellingtook place between the 4th and 8th of September. The event focused on the transformation of how societies deal with natural resources in a world where biodiversity and ecosystem services are at high risk.
The ECEM 2023 continued a series of conferences launched by the European chapter of ISEM, the International Society for Ecological Modelling. ISEM promotes the international exchange of ideas, scientific results, and general knowledge in the areas of systems’ analysis and simulations in ecology, and the application of ecological modelling for natural resource management.
📢Shutout to all attending the #ECEM23@ECEM_2023#ecological#modelling conference TODAY in Leipzig! Make sure to visit the poster session during lunch & find about the unique article types welcome to our #journal! 💡They intend to disseminate models PRIOR TO implementation! https://t.co/dUVskYFK11
— Food & Ecological Systems Modelling Journal, FESMJ (@FESMJournal) September 5, 2023
The Bundesinstitut für Risikobewertung team presented a poster on the Formal Model format and potential new MiDox formats, unique publication types that can be submitted to Pensoft’s Food and Ecological Modelling Journal.
118th Congress of the Italian Botanical Society
Speakers at the 118th Congress of the Italian Botanical Society.
Pensoft was proud to sponsor the 118th Congress of the Italian Botanical Society, which took place in Pisa, Italy from the 13th to 16th of September. Experts in various fields of Botany gathered to share their research on the following topics:
Journals promoted by Pensoft at the 94th Annual Meeting of the Paläontologische Gesellschaft.
Summer may be well and truly over, but as a new academic year begins, Pensoft looks forward to attending more conferences, rewarding more incredible research, and connecting with more of the scientific community. Thank you to everyone who contributed to or engaged with Pensoft’s open-access journals this year, and here’s to a successful final quarter of 2023.
In the ever-evolving landscape of academic publishing, comprehensive and informative citation metrics can make all the difference. Pensoft, the scholarly publisher and technology provider, and the innovative scite.ai platform, have partnered to provide a novel service that is looking to change the way readers perceive and utilise citation data.
scite.ai has been making waves in the scholarly world with its pioneering approach to citation metrics. At the heart of their offering are two distinctive badges, elegantly displayed on the article’s page to let readers gain deeper insights into how a publication is cited by other indexed works.
Each citation is categorized as Supporting, Contrasting, or Mentioning, based on the context of surrounding sentences within the citing publication. This way, anyone can explore not just how many times a document has been cited but also why.
The feature is already accessible under the Metrics tab of any research paper published by a Pensoft journal. The first scite.ai badge displays the number of citations, breaking them down into Supporting, Contrasting, or Mentioning; the second one offers insights on the sections of an article where the citations were featured.
At Pensoft, we are confident that this new functionality enhances the discoverability and contextual richness of articles published in our journals. The integration also empowers Pensoft’s users to gain deeper insights into their research. Whether you’re a scientist seeking to validate your research or a reader in search of authoritative sources, this new feature promises to enrich your academic journey.
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Stay up to date with the latest integrations and features available at journals published by Pensoft by following ARPHA Platform on Twitter and Linkedin.
Today, 16 September 2023, we are celebrating our tenth anniversary: an important milestone that has prompted us to reflect on the incredible journey thatBiodiversity 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.
“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.
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.
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 mannerin 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:
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.
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.
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-proofthe 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 thecollaboration betweenKnowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisherPensoft.
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,”
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 fragmentsof 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 Iin 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!
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.
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.
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 supportmeasures 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, institutionalor 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!
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?
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.
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* 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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Fossil Record – the paleontological scholarly journal of the Natural History Museum of Berlin (Museum für Naturkunde Berlin) published its first articles after moving to the academic publisher Pensoft and its publishing platform ARPHA Platform in late 2021. The renowned scientific outlet – launched in 1998 – joined two other historical journals owned by the Museum: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution, which moved to Pensoft back in 2014.
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.
As a result of the move to ARPHA, Fossil Record utilises 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. A major advantage is that the whole editorial process, starting from the submission of a manuscript and continuing into peer review, editing, publication, dissemination, archiving and hosting, happens within the online ecosystem of ARPHA.
As soon as they are published, the articles in Fossil Record are available in three formats: PDF, machine-readable JATS XML and semantically enriched HTML for better and mobile-friendly reader experience.
The publications are equipped with real-time metrics on both article and sub-article level that allow easy access to the number of visitors, views and downloads for every article and each of it’s figures, tables or supplementary materials. In their turn, the semantic enhancements do not only allow for easy navigation throughout the text and quick access to cited literature and the article’s own citations, but also tag each taxon that appears in the paper to provide links to further information concerning its occurrences, genomics, nomenclature, treatments and more as available from various databases.
The first five papers – now available on the brand new journal website powered by ARPHA – already demonstrate the breadth of topics covered by Fossil Record, including systematics, paleobiogeography, palaeodiversity and morphology, as well as the international appeal of the scholarly outlet. The articles are co-authored by collaborative research teams representing ten countries and spanning three continents: Europe, Asia and Africa.
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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.
