Category: Food and Ecological Systems Modelling Journal (FESMJ)

Here’s to a year of growing and succeeding together!

Within and beyond our Pensoft team, we celebrate a year of well-nourished partnerships and excitement for the future

Yet another hectic year has passed for our team at Pensoft, so it feels right to look back at the highlights from the last 12 months, as we buckle up for the leaps and strides in 2025.

In the past, we have used the occasion to take you back to the best moments of our most popular journals (see this list of 2023 highlights from ZooKeys, MycoKeys, PhytoKeys and more!); share milestones related to our ARPHA publishing platform (see the new journals, integrations and features from 2023); or let you reminisce about the coolest research published across our journals during the year (check out our Top 10 new species from 2021).

In 2022, when we celebrated our 30th anniversary on the academic scene, we extended our festive spirit throughout the year as we dived deep into those fantastic three decades. We put up Pensoft’s timeline and finished the year with a New Species Showdown tournament, where our followers on (what was back then) Twitter voted twice a week for their favourite species EVER described on the pages of our taxonomic journals.

Spoiler alert: we will be releasing our 2024 Top 10 New Species on Monday, 23 December, so you’d better go to the right of this screen and subscribe to our blog!

As we realised we might’ve been a bit biased towards our publishing activities over the years, this time, hereby, we chose to present you a retrospection that captures our best 2024 moments from across the departments, and shed light on how the publishing, technology and project communication endeavours fit together to make Pensoft what it is.

In truth, we take pride in being an exponentially growing family of multiple departments that currently comprises over 60 full-time employees and about a dozen freelancers working from all corners of the world, including Australia, Canada, Belgium and the United Kingdom. Together, we are all determined to make sure we continuously improve our service to all who have trusted us: authors, reviewers, editors, client journals, learned societies, research institutions, project consortia and other external collaborators.


After all, great deeds are only possible when you team up with great like-minded people!

Pensoft as an open-access academic publisher 

Pensoft’s stand at the 2024 TDWG-SPNHC joint conference (September, Japan).

In 2024, at Pensoft, we were hugely pleased to see a significant growth in the published output at almost all our journals, including record-breaking numbers in both submissions and publications at flagship titles of ours, including the Biodiversity Data Journal, PhytoKeys and MycoKeys. 

Other fantastic news came in June from our Indexing team, who confirmed that One Ecosystem: a quite unique and novel academic outlet we launched in collaboration with the Ecosystem Services Partnership in 2016 – received its first Impact Factor. 

Later in 2024, our colleagues, who work together with our clients to ensure their journals comply with the requirements of the top scholarly databases before they apply for indexation, informed us that another two journals in our portfolio have had their applications to Clarivate’s Web of Science successfully accepted. These are the newest journal of the International Association of Vegetation Science: Vegetation and Classification, and Metabarcoding and Metagenomics: a journal we launched in 2017 in collaboration with a team of brilliant scientists working together at the time within the DNAquaNet COST Action.

In 2024, we also joined the celebrations of our long-time partners at the Museum für Naturkunde Berlin, whose three journals: Zoosystematics and Evolution, Deutsche Entomologische Zeitschrift and Fossil Record are all part of our journal portfolio. This year marked the 10th Open Access anniversary of the three journals.

10 years of Open Access: Museum für Naturkunde Berlin and Pensoft celebrate a decade of partnership

In the meantime, we also registered a record in new titles either joining the Pensoft portfolio or opting for ARPHA Platform’s white-label publishing solution, where journal owners retain exclusivity for the publication of their titles, yet use ARPHA’s end-to-end technology and as many human-provided services as necessary.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev with Prof. Dr. Marc Stadler, Editor-in-Chief of IMA Fungus and President of the International Mycological Association at the Pensoft booth at the 12th International Mycological Congress (August, the Netherlands). 

Amongst our new partners are the International Mycological Association who moved their official journal IMA Fungus to ARPHA Platform. As part of Pensoft’s scholarly portfolio, the renowned journal joins another well-known academic title in the field of mycology: MycoKeys, which was launched by Pensoft in 2011. The big announcement was aptly made public at this year’s 12th International Mycological Congress where visitors of the Pensoft stand could often spot newly elected IMA President and IMA Fungus Chief editor: Marc Stadler chatting with our founder and CEO Lyubomir Penev by the Pensoft/MycoKeys booth.

Other partners who chose the services of ARPHA Platform for their journals in 2024 include the International Biogeography Society, United Arab Emirates University and Medical University Pleven.

On our end, we did not stop supporting enthusiastic and proactive scientists in their attempt to bridge gaps in scientific knowledge. In January, we launched the Estuarine Management and Technologies journal together with Dr. Soufiane Haddout of the Ibn Tofail University, Morocco. 

Later on, Dr. Franco Andreone (Museo Regionale di Scienze Naturali, Italy) sought us with the idea to launch a journal addressing the role of natural history museums and herbaria collections in scientific progress. This collaboration resulted in the Natural History Collections and Museomics journal, officially announced at the joint TDWG-SPNHC conference in Okinawa, Japan in August.

Natural History Collections and Museomics launches with its inaugural editorial

Around this time, we finalised our similarly exciting journal project in partnership with Prof. Dr. Volker Grimm (UFZ, Germany), Prof. Dr. Karin Frank (UFZ, Germany), Prof. Dr. Mark E. Hauber (City University of New York) and Prof. Dr. Florian Jeltsch (University of Potsdam, Germany). The outcome of this collaboration is called Individual-based Ecology: a journal that aims to promote an individual-based perspective in ecology, as it closes the knowledge gap between individual-level responses and broader ecological patterns.

ARPHA Platform welcomes new journal launched by Pensoft: Individual-based Ecology

The three newly-launched journals are all published under the Diamond Open Access model, where neither access, nor publication is subject to charges.

As you can see, we have a lot to be proud of in terms of our journals. This is also why in 2024 our team took a record number of trips to attend major scientific events, where we got the chance to meet face-to-face with long-time editors, authors, reviewers and readers of our journals. Even more exciting was meeting the new faces of scientific research and learning about their own take on scholarship and academic journals.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev welcomed editors at PhytoKeys to the Pensoft-PhytoKeys-branded booth at the XX International Botanical Congress in July 2024 (Spain).

In 2024, we presented our journals and publishing opportunities at about 20 scientific forums, including the XX International Botanical Congress (July, Spain), the 12th International Mycological Congress (August, the Netherlands), the 10th World Congress of Herpetology (August, Malaysia) and the XXVII International Congress of Entomology (August, Japan).

Pensoft as a scientific technology provider

We cannot possibly comment on Pensoft’s tech progress in 2024 without mentioning the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library) that we coordinated for three years ending up last April. 

This 36-month endeavour saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. 

Following these three years of collaborative work, we reported a great many notable research outputs from our consortium (find about them in the open-science project collection in the Research Ideas and Outcomes journal, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective”) that culminated in the Biodiversity Knowledge Hub: a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks; and also a set of policy recommendations addressing key policy makers, research institutions and funders who deal with various types of data about the world’s biodiversity, and are thereby responsible to ensuring there findability, accessibility, interoperability and reusability (FAIR-ness).

The Biodiversity Knowledge Hub
Visit the Biodiversity Knowledge Hub: the main product of the BiCIKL consortium at: https://biodiversityknowledgehub.eu/.

Apart from coordinating BiCIKL, we also worked side-by-side with our partners to develop, refine and test each other’s tools and services, in order to make sure that they communicate efficiently with each other, thereby aligning with the principles of FAIR data and the needs of the scientific community in the long run.

During those three years we made a lot of refinements to our OpenBiodiv: a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System, and our ARPHA Writing Tool. The latter is an XML-based online authoring environment using a large set of pre-formatted templates, where manuscripts are collaboratively written, edited and submitted to participating journals published on ARPHA Platform. What makes the tool particularly special is its multiple features that streamline and FAIRify data publishing as part of a scientific publication, especially in the field of biodiversity knowledge. In fact, we made enough improvements to the ARPHA Writing Tool that we will be soon officially releasing its 2.0 version!

OpenBiodiv – The Open Biodiversity Knowledge Management System
ARPHA Writing Tool 2.0

Amongst our collaborative projects are the Nanopublications for Biodiversity workflow that we co-developed with KnowledgePixels to allow researchers to ‘fragment’ their most important scientific findings into machine-actionable and machine-interpretable statements. Being the smallest units of publishable information, these ‘pixels of knowledge’ present an assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, its original source (provenance) and citation record (publication info).

Nanopublications for Biodiversity

In partnership with the Swiss-based Text Mining group of Patrick Ruch at SIB and the text- and data-mining association Plazi, we brought the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

Towards the “Biodiversity PMC”: a literature database supporting advanced content queries

Understandably, we spent a lot of effort, time and enthusiasm in raising awareness about our most recent innovations, in addition to our long-standing workflows, formats and tools developed with the aim to facilitate open and efficient access to scientific data; and their integration into published scholarly work, as well as receiving well-deserved recognition for their collection.

We just can’t stress it enough how important and beneficial it is for everyone to have high-quality FAIR data, ideally made available within a formal scientific publication!    

Pensoft’s CTO Teodor Georgiev talks about innovative methods and good practices in the publication of biodiversity data in scholarly papers at the First national meeting of the Bulgarian Barcode of Life (BgBOL) consortium (December, Bulgaria).
Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev presenting his “Data papers on biodiversity” talk at the “Biodiversity data in montane and arid Eurasia” symposium jointly organized by GBIF and by the Institute of Zoology of Republic of Kazakhstan (November, Kazakhstan).

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Pensoft’s CTO Teodor Georgiev presents new features and workflows currently in testing at the ARPHA Writing Tool 2.0 at the EASE Autumn Symposium 2024 (online event).

Pensoft’s Head of Journal development, Marketing and PR Iva Boyadzhieva talks about Pensoft’s data publishing approach and innovations at the German Ecological Society 53rd Annual Conference (September, Germany).

Pensoft as a science communicator

At our Project team, which is undoubtedly the fastest developing department at Pensoft, science communicators are working closely with technology and publishing teams to help consortia bring their scientific results closer to policy actors, decision-makers and the society at large.

Ultimately, bridging the notorious chasm between researchers and global politics boils down to mutual understanding and dialogue. 

Pensoft’s communication team attended COP16 (November 2024, Colombia) along with partners at the consortia of CO-OP4CBD, BioAgora and RESPIN: three Horizon Europe projects, whose communication and dissemination is led by Pensoft.

Throughout 2024, the team, comprising 20 science communicators and project managers, has been working as part of 27 EU-funded project consortia, including nine that have only started this year (check out all partnering projects on the Pensoft website, ordered from most recently started to oldest). Apart from communicating key outcomes and activities during the duration of the projects, at many of the projects, our team has also been actively involved in their grant proposal drafting, coordination, administration, platform development, graphic and web design and others (see all project services offered by Pensoft to consortia).

Naturally, we had a seat on the front row during many milestones achieved by our partners at all those 27 ongoing projects, and communicated to the public by our communicators. 

Amongst those are the release of the InsectsCount web application developed within the Horizon 2020 project SHOWCASE. Through innovative gamification elements, the app encourages users to share valuable data about flower-visiting insects, which in turn help researchers gain new knowledge about the relationship between observed species and the region’s land use and management practices (learn more about InsectsCount on the SHOWCASE prroject website). 

Another fantastic project output was the long-awaited dataset of maps of annual forest disturbances across 38 European countries derived from the Landsat satellite data archive published by the Horizon Europe project ForestPaths in April (find more about the European Forest Disturbance Atlas on the ForestPaths project website).

In a major company highlight, last month, our project team participated in COP29 in Baku, Azerbaijan with a side event dedicated to the role of open science and science communication in climate- and biodiversity-friendly policy.

Pensoft’s participation at COP29 – as well as our perspective on FAIR data and open science – were recently covered in an interview by Exposed by CMD (a US-based news media accredited to cover the event) with our science communicator Alexandra Korcheva and project manager Boris Barov. 

You see, A LOT of great things worth celebrating happened during the year for us at Pensoft: all thanks to ceaselessly flourishing collaboration based on transparency, trust and integrity. Huge ‘THANK YOU!’ goes to everyone who has joined us in our endeavours!

Here’s to many more shared achievements coming up in 2025!

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Pensoft took a BiCIKL ride to Naturalis to report on a 3-year endeavour towards FAIR data

Three years ago, the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data.

Leiden – also known as the ‘City of Keys’ and the ‘City of Discoveries’ – was aptly chosen to host the third Empowering Biodiversity Research (EBR III) conference. The two-day conference – this time focusing on the utilisation of biodiversity data as a vehicle for biodiversity research to reach to Policy – was held in a no less fitting locality: the Naturalis Biodiversity Center. 

On 25th and 26th March 2024, the delegates got the chance to learn more about the latest discoveries, trends and innovations from scientists, as well as various stakeholders, including representatives of policy-making bodies, research institutions and infrastructures. The conference also ran a poster session and a Biodiversity Informatics market, where scientists, research teams, project consortia, and providers of biodiversity research-related services and tools could showcase their work and meet like-minded professionals.

BiCIKL stops at the Naturalis Biodiversity Center

The main outcome of the BiCIKL project: the Biodiversity Knowledge Hub, a one-stop knowledge portal to interlinked and machine-readable FAIR data.

The famous for its bicycle friendliness country also made a suitable stop for BiCIKL (an acronym for the Biodiversity Community Integrated Knowledge Library): a project funded under the European Commission’s Horizon 2020 programme that aimed at triggering a culture change in the way users access, (re)use, publish and share biodiversity data. To do this, the BiCIKL consortium set off on a 3-year journey to build on the existing biodiversity data infrastructures, workflows, standards and the linkages between them.

Many of the people who have been involved in the project over the last three years could be seen all around the beautiful venue. Above all, Naturalis is itself one of the partnering institutions at BiCIKL. Then, on Tuesday, on behalf of the BiCIKL consortium and the project’s coordinator: the scientific publisher and technology innovator: Pensoft, Iva Boyadzhieva presented the work done within the project one month ahead of its official conclusion at the end of April.

As she talked about the way the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data, she focused on BiCIKL’s main outcome: the Biodiversity Knowledge Hub (BKH).

Key results from the BiCIKL project three years into its existence presented by Pensoft’s Iva Boyadzhieva at the EBR III conference.

Intended to act as a knowledge broker for users who wish to navigate and access sources of open and FAIR biodiversity data, guidelines, tools and services, in practicality, the BKH is a one-stop portal for understanding the complex but increasingly interconnected landscape of biodiversity research infrastructures in Europe and beyond. It collates information, guidelines, recommendations and best practices in usage of FAIR and linked biodiversity data, as well as a continuously expanded catalogue of compliant relevant services and tools.

At the core of the BKH is the FAIR Data Place (FDP), where users can familiarise themselves with each of the participating biodiversity infrastructures and network organisations, and also learn about the specific services they provide. There, anyone can explore various biodiversity data tools and services by browsing by their main data type, e.g. specimens, sequences, taxon names, literature.

While the project might be coming to an end, she pointed out, the BKH is here to stay as a navigation system in a universe of interconnected biodiversity research infrastructures.

To do this, not only will the partners continue to maintain it, but it will also remain open to any research infrastructure that wishes to feature its own tools and services compliant with the linked and FAIR data requirements set by the BiCIKL consortium.

On the event’s website you can access the BiCIKL’s slides presentation as presented at the EBR III conference.

What else was on at the EBR III?

Indisputably, the ‘hot’ topics at the EBR III were the novel technologies for remote and non-invasive, yet efficient biomonitoring; the utilisation of data and other input sourced by citizen scientists; as well as leveraging different types and sources of biodiversity data, in order to better inform decision-makers, but also future-proof the scientific knowledge we have collected and generated to date.

Project’s coordinator Dr Quentin Groom presents the B-Cubed’s approach towards standardised access to biodiversity data for the use of policy-making at the EBR III conference.

Amongst the other Horizon Europe projects presented at the EBR III conference was B-Cubed (Biodiversity Building Blocks for policy). On Monday, the project’s coordinator Dr Quentin Groom (Meise Botanic Garden) familiarised the conference participants with the project, which aims to standardise access to biodiversity data, in order to empower policymakers to proactively address the impacts of biodiversity change.

You can find more about B-Cubed and Pensoft’s role in it in this blog post.

On the event’s website you can access the B-Cubed’s slides presentation as presented at the EBR III conference.

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Dr France Gerard (UK Centre for Ecology & Hydrology) talks about the challenges in using raw data – including those provided by drones – to derive habitat condition metrics.

MAMBO: another Horizon Europe project where Pensoft has been contributing with expertise in science communication, dissemination and exploitation, was also an active participant at the event. An acronym for Modern Approaches to the Monitoring of BiOdiversity, MAMBO had its own session on Tuesday morning, where Dr Vincent Kalkman (Naturalis Biodiversity Center), Dr France Gerard (UK Centre for Ecology & Hydrology) and Prof. Toke Høye (Aarhus University) each took to the stage to demonstrate how modern technology developed within the project is to improve biodiversity and habitat monitoring. Learn more about MAMBO and Pensoft’s involvement in this blog post.

MAMBO’s project coordinator Prof. Toke T. Høye talked about smarter technologies for biodiversity monitoring, including camera traps able to count insects at a particular site.

On the event’s website you can access the MAMBO’s slides presentations by Kalkman, Gerard and Høye, as presented at the EBR III conference.

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The EBR III conference also saw a presentation – albeit remote – from Prof. Dr. Florian Leese (Dean at the University of Duisburg-Essen, Germany, and Editor-in-Chief at the Metabarcoding and Metagenomics journal), where he talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. 

Amongst the key tasks here, he pointed out, are the alignment of DNA-based methods with the Global Biodiversity Framework; central push and funding for standards and guidance; publication of data in portals that adhere to the best data practices and rules; and the mobilisation of existing resources such as the meteorological ones. 

Prof. Dr. Florian Leese talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. He also referred to the 2022 Forum Paper: “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al.

He also made a reference to the Forum Paper “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al., where the international team provided a brief rationale and an overview of guidelines targeting the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. In the study, published in the Metabarcoding and Metagenomics journal in 2022, they also introduced a living version of these guidelines, which continues to encourage feedback and interaction as new techniques and best practices emerge.

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You can find the programme on the conference website and see highlights on the conference hashtag: #EBR2024.

Don’t forget to also explore the Biodiversity Knowledge Hub for yourself at: https://biodiversityknowledgehub.eu/ 

Moving towards a systems-based Environmental Risk Assessment for wild bees, butterflies, moths and hoverflies: Pensoft joins PollinERA

Pensoft will lead the communication, dissemination and exploitation activities of the Horizon Europe project, which aims to reverse pollinator population declines and reduce impacts of pesticides.

The European Green Deal, the EU biodiversity strategy, the EU zero pollution action plan, and the revised EU pollinators initiative all indicate the need to protect pollinators and address insect and pollinator declines.

Plant protection products (PPP), also known as pesticides, have been identified as one of the primary triggers of pollinator decline. However, significant knowledge gaps and critical procedural limitations to current pesticide risk assessment require attention before meaningful improvements can be realised. The functional group is currently represented by only one species, the honey bee, which does not necessarily share other species’ biological and ecological traits.

Coordinated by The Social-Ecological Systems Simulation (SESS) Centre, Aarhus University and Prof. Christopher J. Topping, PollinERA (Understanding pesticide-Pollinator interactions to support EU Environmental Risk Assessment and policy) aims to move the evaluation of the risk and impacts of pesticides and suggestions for mitigation beyond the current situation of assessing single pesticides in isolation on honey bees to an ecologically consistent assessment of effects on insect pollinators.

This will be achieved through the development of a new systems-based environmental risk assessment (ERA) scheme, tools and protocols for a broad range of toxicological testing, feeding to in silico models (QSARS, toxicokinetic/toxicodynamic, and ALMaSS agent-based population simulations). 

Using a strong stakeholder co-development approach, these models will be combined in a One System framework for risk assessment and policy evaluation including an international long-term monitoring scheme for pollinators and pesticides. 

The One System framework builds on the recent roadmap for action on the ERA of chemicals for insect pollinators, developed within the IPol‐ERA project, funded by the European Food Safety Authority (EFSA). The framework will expand the ERA tools currently used for honey bees to include wild bees, butterflies, moths and hoverflies.

With an overall goal of reversing pollinator population declines and reducing the harmful impacts of pesticides, for the next four years, PollinERA will follow four specific objectives:

  1. Fill ecotoxicological data gaps to enable realistic prediction of the source and routes of exposure and the impact of pesticides on pollinators and their sensitivity to individual pesticides and mixtures.
  2. Develop and test a co-monitoring scheme for pesticides and pollinators across European cropping systems and landscapes, developing risk indicators and exposure information.
  3. Develop models for predicting pesticide toxicological effects on pollinators for chemicals and organisms, improve toxicokinetic/toxicodynamic (TKTD) and population models, and predict environment fate.
  4. Develop a population-level systems-based approach to risk and policy assessment considering multiple stressors and long-term spatiotemporal dynamics at a landscape scale and generate an open database for pollinator/pesticide data and tools.
Between 17 and 18 January 2024, experts from various realms of knowledge – from pollinator ecology, pesticide exposure and toxicological testing, to stakeholder engagement and communications – gathered in Aarhus, Denmark, to officially launch PollinERA. The two-day event seeded fruitful discussions on the project’s specific objectives, mission, methodology, outcomes and expected results.

With more than 20 years of experience in science communication, Pensoft is leading Work Package 6: Communication, Dissemination and Exploitation, that will ensure the effective outreach of PollinERA to its multiple target audiences. Based on the tailor-made communication, dissemination, exploitation and engagement strategies, Pensoft will provide a recognisable visual identity of the project, along with a user-friendly website, social media profiles, promotional materials, newsletters, infographics and videos. Pensoft will also contribute to the stakeholder mapping process and the organisation of various workshops and events.

To support the proactive, open-science transfer of results and scientific achievements, two PollinERA topical collections of articles will be established in Pensoft’s Food and Ecological Systems Modelling Journal (FESMJ) and the Research Ideas and Outcomes (RIO) journal.

PollinERA’s coordinator Prof. Christopher J. Topping (The Social-Ecological Systems Simulation Centre, Aarhus University) gave a warm welcome during the kick-off meeting of the project in Aarhus, Denmark.

In a joint effort to maximise impact and ensure sustainability of results, PollinERA will unfold in close collaboration with the sister Horizon Europe-funded project WildPosh, where Pensoft is also leading the Communication, dissemination and exploitation work package. 

Coordinated by Prof. Denis Michez (University of Mons), WildPosh aims to significantly improve the evaluation of risk to pesticide exposure of wild pollinators, and enhance the sustainable health of pollinators and pollination services in Europe.

Collaboration mechanisms between the PollinERA and the WildPosh projects include joint communication activities and events, joint data management strategy and alignment of activities to solidify the quality of final outputs.

Prof. Denis Michez (University of Mons), the coordinator of PollinERA’s sister-project WildPosh, presented the missions, objectives and methods, as well as the similarities, differences and collaboration potential between the two projects at PollinERA’s kick-off meeting in Aarhus, Denmark.

“It is fantastic that the European Commission puts so much effort into preserving wild pollinators and the countless benefits they bring to our society! The One System framework will hopefully become a fundamental part for the environmental risk assessment of chemicals for insect pollinators. I am really looking forward to implementing this insightful project, in close collaboration with its sister project WildPosh, where Pensoft is leading the dissemination efforts as well.”

says Teodor Metodiev, Principal Investigator for Pensoft at both PollinERA and WildPosh.

The PollinERA consortium comprises partners from eight European countries that represent a diverse range of scientific disciplines spanning from pollinator ecology, pesticide exposure and toxicological testing, to stakeholder engagement and communications.

Consortium:
  1. Aarhus University
  2. Jagiellonian University
  3. Lund University
  4. University of Bologna
  5. Osnabrück University
  6. Institute of Nature Conservation of the Polish Academy of Sciences
  7. Mario Negri Institute for Pharmacological Research
  8. BeeLife European Beekeeping Coordination
  9. Swedish University of Agricultural Sciences
  10. Pensoft Publishers
  11. Zip Solutions

Stay up to date with the PollinERA project’s progress on X/Twitter (@pollinERA_eu) and LinkedIn (/pollinera-eu).

Assessment, monitoring, and mitigation of chemical stressors on the health of wild pollinators: Pensoft joins WildPosh

  

Pensoft collaborates with R Discovery to elevate research discoverability

Pensoft and R Discovery’s innovative connection aims to change the way researchers find academic articles.

Leading scholarly publisher Pensoft has announced a strategic collaboration with R Discovery, the AI-powered research discovery platform by Cactus Communications, a renowned science communications and technology company. This partnership aims to revolutionize the accessibility and discoverability of research articles published by Pensoft, making them more readily available on R Discovery to its over three million researchers across the globe.

R Discovery, acclaimed for its advanced algorithms and an extensive database boasting over 120 million scholarly articles, empowers researchers with intelligent search capabilities and personalized recommendations. Through its innovative Reading Feed feature, R Discovery delivers tailored suggestions in a format reminiscent of social media, identifying articles based on individual research interests. This not only saves time but also keeps researchers updated with the latest and most relevant studies in their field.

Open Science is much more than cost-free access to research output.

Lyubomir Penev

One of R Discovery’s standout features is its ability to provide paper summaries, audio readings, and language translation, enabling users to quickly assess a paper’s relevance and enhance their research reading experience significantly.

With over 2.5 million app downloads and upwards of 80 million journal articles featured, the R Discovery database is one of the largest scholarly content repositories.

“At Pensoft, we do realise that Open Science is much more than cost-free access to research outputs. It is also about easier discoverability and reusability, or, in other words, how likely it is for the reader to come across a particular scientific publication and, as a result, cite and build on those findings in his/her own studies. By feeding the content of our journals into R Discovery, we’re further facilitating the discoverability of the research done and shared by the authors who trust us with their work,” said ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev.

Abhishek Goel, Co-Founder and CEO of Cactus Communications, commented on the collaboration, “We are delighted to work with Pensoft and offer researchers easy access to the publisher’s high-quality research articles on R Discovery. This is a milestone in our quest to support academia in advancing open science that can help researchers improve the world.”

So far, R Discovery has successfully established partnership with over 20 publishers, enhancing the platform’s extensive repository of scholarly content. By joining forces with R Discovery, Pensoft solidifies its dedication to making scholarly publications from its open-access, peer-reviewed journal portfolio easily discoverable and accessible.

Science in the sunshine: Pensoft’s month of European conferences

Pensoft participated in five conferences across Germany and Italy in September 2023.

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.

Wildlife Research and Conservation 2023

Wildlife Research and Conservation 2023 took place in Berlin between the 9th and 11th of September. Jointly organised by the Leibniz Institute for Zoo and Wildlife Research, the European Association of Zoos and Aquaria and WWF Germany, it was a fantastic event, featuring an exchange of ideas between wildlife scientists from different disciplines related to mammalian species.

Image showing the WRC2023 logo and two women promoting Pensoft at a conference.
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.

Man holding a certificate.
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 Switzerland in 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. 

Woman standing beside man.
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. 

The Pensoft team took great pleasure in talking to attendees about their fantastic journals focused on ecology and biodiversity, including Food and Ecological Systems Modelling Journal, Neobiota, Nature Conservation, One Ecosystem, Vegetation Classification and Survey and Research Ideas and Outcomes, as well as meeting with authors, reviewers and editors.

European Conference on Ecological Modelling

Also in Leipzig, the European Conference on Ecological Modelling took 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.

Pensoft presented its innovative journals in the field of ecology and modelling, such as Nature Conservation, Food and Ecological Systems Modelling Journal and Neobiota, as well as the projects PoshBee and B-GOOD, which aim to help beekeepers and support healthy bee populations where Pensoft acts as the dissemination partner.

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

Three men sitting before a projector screen at a conference.
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:

  • Molecular and cell biology
  • Taxonomy, systematics and evolution
  • Biodiversity
  • Environmental monitoring and policies
  • Biotechnology and applied botany
  • Ecology

Pensoft awarded Emma Cocco, University of Cagliari, and Lucrezia Laccetti, University of Naples Federico II, a free article publication in any of Pensoft’s journals related to botany.  Additionally, Silvia Cannucci, University of Siena, and Flavia Guzzi received the Italian Botanical Society’s support for publishing papers in Italian Botanist for their excellent research.

Four people at a certificate presentation.
Best poster award, presented by Pensoft.

94th Annual Meeting of the Paläontologische Gesellschaft

Finally, between the 18th and 22nd of September, the 94th Annual Meeting of the Paläontologische Gesellschaft was held in Jena, Germany. Pensoft couldn’t make it in person, but still made sure to showcase journals publishing papers in palaeontology, especially Zitteliana and Fossil Record. The international meeting was a great success, and focused on cutting-edge research from palaeobiology, palaeontology, geobiology and related subjects.

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.

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Pensoft among the first 27 publishers to share prices & services via the Journal Comparison Service by Plan S

All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research. 

As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service. 

According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.

While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals. 

This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.

“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”

said Robert Kiley, Head of Strategy at cOAlition S. 

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About cOAlition S:

On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.

About Plan S:

Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.

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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Food Modelling Journal: New open-access venue provides a platform for food scientists

The open-access Food Modelling Journal (FMJ) was launched by the AGINFRA+ community and Pensoft with the aim to encourage food science specialists, agronomists and computer scientists to come together and work on assuring and improving food supply, quality and safety in our globalised and rapidly changing world.

An introductory editorial and an article of a unique publication type are already made available in the next-generation journal

The open-access Food Modelling Journal (FMJ) was launched by the AGINFRA+ community and Pensoft with the aim to encourage food science specialists, agronomists and computer scientists to come together and work on assuring and improving food supply, quality and safety in our globalised and rapidly changing world.

The Food Modelling Journal will be focusing on the publication of information objects and digital resources in the food science field, related (but not limited) to: food safety, food quality, food control, food defence and food design, documenting experimental or observational data and mathematical models.

By providing a platform and tools for describing scientific records and crediting for dedicated models, data, data analytics workflows and software, FMJ fosters the overall reproducibility and reusability of research.

FMJ also aims to shed light on what we refer to as research objects – data, software scripts, visualisation routines or models. Usually, they would stay undervalued, underused and uncredited, despite their importance for the scientific progress.

The focus and scope of the journal are supported by a number of specific key features:

  • Quality but not quantity
  • Cross-disciplinary approach
  • Open data and software code policy
  • Rapid turnaround time
  • Advanced open access and machine-readability.

It should be noted that the Open Science movement and the barrier-free access to research, is at the heart of the FMJ project.

To support its authors, the AGINFRA+ community, Pensoft and Food Modelling Journal have provided them access to the ARPHA Writing Tool, where researchers are able to work together with their co-authors, colleagues and peers on manuscripts from the drafting stage to publication.

A FSKX model run using the executable paper feature available in Food Modelling Journal.

A particularly appealing feature, meant to promote reproducibility, collaboration and openness in science, is the executable papers, where users can reproduce research findings using the published model and running it either with default or new parameters. By clicking an “Execute” button within the body of the article, users are taken to an external virtual environment where they will be able to execute the computation. By ‘encapsulating’ all the details needed to perform the action within the paper, this feature ensures that the published findings will remain testifiable in the future.

“While the long-lasting tradition in science used to focus on crediting researchers’ work through conventional research articles and especially by counting their citations, many exciting, useful and often invaluable products of the research cycle, such as data, software scripts, visualisation routines or models (usually called “research objects”) normally stay undervalued, underused and uncredited, despite their importance for scientific progress,” note the editorial board in the introductory editorial.

“The consequences of this neglect of the initial and intermediate steps of the research cycle in favour of the research articles or research books are obvious: scientists often repeat efforts done by others instead of using these as a stepping stone for further analyses and generating new knowledge, let alone the impossible or restricted reproducibility and reusability of research results,” they add.

The first paper of a unique publication type: FSKX (Food Safety Knowledge), is already publicly accessible in the journal. Classified as an early research outcome, the article presents a new generic model for assessing the risk of salmonellosis associated with the consumption of table eggs. To ensure the reusability of the model, the research team of Virginie Desvignes (ANSES – French Food Safety Agency) have made it available in the Food Safety Knowledge Markup Language (FSK-ML) format alongside the executable model script, visualisation script and simulation settings.

FSK-ML is an open information exchange format that is based on harmonised terms, metadata and controlled vocabulary to harmonise annotations of risk assessment models and that was significantly improved and extended during the AGINFRA+ project.

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Food Modelling Journal is indexed by BASE, CNKI, CrossRef, Dimensions, Google Scholar, J-Gate, Mendeley, Microsoft Academic, Naviga (Softweco), OCLC WorldCat, OpenAIRE, OpenCitations, ReadCube, Transpose, Ulrichsweb™ and Unpaywall; and archived at CLOCKSS, Zenodo and Portico.