Category: Research Ideas and Outcomes (RIO Journal)

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).

.

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!

***

Now, to keep up with our next steps in real time, we invite you to follow Pensoft on social media on BlueSky, X, Facebook, Instagram and Linkedin! 

Don’t forget to also enter your email to the right to sign up for new content from this blog!

The Biodiversity Digital Twin to help understand our planet’s life

By combining and improving digitally available data and models, BioDT offers approaches for sustainable biodiversity management and ecosystem conservation.

Biodiversity is essential for the processes that support all life on Earth. It provides critical resources such as food and energy, and supports ecosystem health. However, climate change, deforestation, and pollution are destroying habitats, altering ecosystems, and eliminating – or introducing – species that are fundamental for planet’s biosphere.

To tackle the challenges caused by environmental change and human activities on biodiversity, a consortium of 22 partners led by CSC – IT Center for Science, home of the EuroHPC LUMI supercomputer, is developing Biodiversity Digital Twins (BioDT) as a result of the European Commission’s initiative.

Cover of the “Building Biodiversity Digital Twins” article collection in RIO journal.

The BioDT project aims to revolutionise our understanding of biodiversity dynamics by integrating advanced modelling, simulation, and prediction capabilities. By combining and improving digitally available data and models, BioDT offers approaches for sustainable biodiversity management and ecosystem conservation. BioDT’s combines expertise in biodiversity, ecological modelling, FAIR data, high-performance computing, and artificial intelligence.

BioDT aims to enhance the accuracy and predictive performance of biodiversity models through iterative development and validation against independent data. This approach can be critical for developing decision support tools and policy development. By continuously updating data, BioDT will provide real-time predictions of biodiversity patterns and processes through interactive maps and summaries. The consortium leverages existing technologies and data from major research infrastructures (GBIF, eLTER, DiSSCo, and LifeWatch ERIC) to achieve this goal.

A screenshot of the BioDT homepage.

The project’s impact extends to addressing critical issues, including impact of environmental  change on species and ecosystems, food security, and the implementation of the EU and international policies. The project contributes to the UN Sustainable Development Goals 2 (Zero Hunger), 3 (Good Health and Well-being), 13 (Climate Action), and 15 (Life on Land).

BioDT develops prototype Digital Twins for biodiversity conservation

In order to test its modelling system, BioDT is developing ten prototype digital twins (pDTs) focused on species and ecosystems of high conservation and policy concern, such as invasive species, pollinators and grasslands.
The pDTs are divided into four main groups:

  • Species Response to Environmental Change: focus on the interactions between species and ecosystems. By incorporating temporal dynamics rather than pure space-for-time substitutions, BioDT improves temporal predictions and accuracy. Different sources of uncertainty are quantified using extensive geographic data combined with high-resolution time-series data in a single modelling framework.
  • Genetically Detected Biodiversity: addressing food security and challenging environments by integrating genomic methods based on DNA data with traditional biodiversity data. These twins focus on crop wild relatives and other genetic resources for farming and food security, as well as DNA-detected biodiversity in poorly known habitats.
  • Dynamics of Species of Policy Concern: applying modelling and high-performance computing to invasive and alien species recognised at EU and national levels. This twin involves using current species occurrence data, and tackling crucial environmental conditions and invasive effects on native taxa and ecosystems.
  • Influence of Species Interactions: predicting disease outbreaks using vector species and exploring the patterns and processes of insect pollinators. Work on interaction twins involves further development of data exchange models and establishing temporal historic reference points through digitisation of collection specimens.
A screenshot from the BioDT homepage showing the purposes of prototype digital twins.

The pDTs aim to make essential datasets, best practices, expertise, and lessons learned available and ready for use to researchers and research infrastructures in implementing the use cases, while providing.

The pDTs test the models predictive performance and data availability scenarios, and apply them to address biodiversity challenges through scenario simulations, predictions, and biomonitoring methods. This iterative approach aims to integrate and compare the predictive performance of various modelling approaches, stimulating the development of next-generation prototypes.

To learn more about the biodiversity pDTs, explore the dedicated pages on the BioDT website

Building Biodiversity Digital Twins: a BioDT collection of scientific papers

To further advance the development and reliability of Biodiversity Digital Twins, the BioDT team has produced 10 scientific papers, compiled in the “Building Biodiversity Digital Twins” issue of the open-science scholarly journal Research Ideas and Outcomes (RIO).

“The collection offers an in-depth understanding of the conceptual and technical advancements achieved towards developing digital twins for a wide range of biodiversity topics. Through the BioDT project, we are enabling a broad audience to interactively understand and predict biodiversity changes across space and time.” says Gabriela Zuquim, Scientific Coordinator at CSC for the BioDT project 

The collection serves as a centralised access point to project outputs by the BioDT initiative. Publication of rather unconventional and not traditionally published research outputs is in fact amongst the unique features of the open-science RIO journal. Another feature is the possibility of individual publications to be mapped to the SDGs they contribute to, thereby further underlining their significance.

A conceptual diagram of a digital twin prototype from this paper. The core aim of this project is to test the feasibility of generating essentially real-time updating predictions on bird spatiotemporal distributions and singing activity by combining prior information, based on long-term monitoring data with continuously accumulating new information provided by citizen scientists.

In the case of BioDT, RIO has made it possible for the project team to illustrate the process of prototyping Biodiversity Digital Twins in the format of a peer-reviewed scientific article, thereby ensuring its discoverability, credibility, citability, reusability and long-term public availability. By opting for this transparent approach to sharing their scientific work that has standed the rigour of formal scientific review, the BioDT project ensures that future scientists can make better and more efficient use of the models developed by the consortium’s researchers, data, and cutting-edge technology.

For example, one publication describes the HONEYBEE Prototype Digital Twin. The prototype will allow, after the ongoing calibration with land use and hive weight data,  predictions of honeybee population dynamics, mite infestation and honey production. The model was developed based on a previously developed one, devised to simulate foraging of a single bee colony. By using the prototype digital twin, users can interactively apply the model on various time and geographic scales ranging from local sites to whole regions or even country level. Thus, it can become an essential tool for the assessment of the viability and productivity of honey bee colonies around Germany, regardless of the specificity of landscapes and management strategies.

Overview of the prototype HONEYBEE-pDT

Our vision is that the assessment can even be run to take into account different climate-change scenarios. The publication also provides guidelines to potential users of the prototype. The authors of the paper, led by Dr Jürgen Groeneveld (Helmholtz Centre for Environmental Research – UFZ, Germany) reminds that despite honey bees “being a managed species, they are severely affected by climate change, emerging parasites and diseases, modern agricultural land use and possibly inappropriate beekeeping practices”, while going on to cite worrying data about the trends in both Europe and the USA. 

Similarly, other publications already available from the collection address equally crucial and pressing issues with impact on a global scale, including disease outbreaks, crop management, invasive species, bird and vegetation dynamics. 

“The Building Biodiversity Digital Twins collection of project papers suited our needs perfectly,” said Dmitry Schigel, GBIF Scientific officer and a coordinating editor of the collection. “The project team agreed to capture the project’s iterations and reveal our two-thirds stage prototypes two years into the project with one more to go. The innovative platform that the Pensoft’s RIO journal provides lets us describe our progress in a less formal but still peer-reviewed setting. Thanks to the efficient work of the author teams, reviewers and co-editors, this special issue came together quickly and now enables our prototype digital twin teams to attract and process feedback from broader audiences”

Explore the “Building Biodiversity Digital Twins” collection, freely accessible on Pensoft’s RIO Journal. Read them now and see their impact!

Innovative tools for science communication: How to increase your research impact

At the 5th ESP Europe conference in Wageningen, Pensoft will lead a training session on effective science communication through open access publishing.

The Ecosystem Services Partnership (ESP) is a global network that connects ecosystem services scientists, practitioners, stakeholders, and policymakers at local, national, regional, and global scales. ESP enhances and encourages a diversity of approaches, while reducing unnecessary duplication of effort in the development of concepts and application of ecosystem services.

Starting in 2008, ESP organises annual international conferences, where experts share research progress and exchange ideas in the field of ecosystem services, strengthening cooperation among scientists and practitioners. Since 2015, global and regional conferences started taking place bi-annually, with the 5th ESP Europe conference taking place this year between 18 and 22 November in Wageningen, The Netherlands, under the theme ‘Ecosystem Services: One Planet, One Health’.

The ESP Europe conference will focus on the question of how the ecosystem services concept can address the challenges involved in delivering the global vision of One Health. It will also highlight the interdependence of health across various domains – human, animal, plant, and ecosystem health, and the health of the global environment.

In addition to the main event, the organisers are providing access to pre-conference trainings on Sunday, 17 November, one day before the official start of the conference. One of these focuses on science communication and its role in enhancing research impact. Titled “Innovative tools for science communication: How to increase your research impact”, this session will be hosted by Pensoft Publishers.

A communication and dissemination leader in a wide range of EU research projects, as well as an independent publishing company, Pensoft will introduce the participants to best practices in science communication, drawing examples from a project portfolio which covers ecosystems and biodiversity, agriculture and forestry, pollinators and more. This training activity will also highlight the integral role of open science in effective dissemination, showcasing the opportunities facilitated by Pensoft’s open-access journals, which promoting transparency, accessibility, and reusability of results. Overall, the session will provide an in-depth look into the interlinkage between effectively communicated research outputs and the benefits of openly published data.

The Pensoft team will share their experiences with projects such as  SELINA and SpongeBoost, both of which will also be presented in the scientific sessions and via a shared booth at the event.

Everyone who has already registered for the official programme can still add a training to their application using this link.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

***

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

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

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

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

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.

***

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.

***

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.

***

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 partners with ResearchGate to drive readership and visibility of open access journals

Content from 20 Pensoft journals will now be automatically added to ResearchGate to reach the research network’s 25 million users. Each journal will also receive a dedicated profile.

ResearchGate, the professional network for researchers, and Pensoft today announced a new partnership that will see a set of Pensoft’s open access journals increase their reach and visibility through ResearchGate – increasing access and engagement with its 25 million researcher members.  

Pensoft is a fully open access publisher, providing high-quality end-to-end services to its own and third-party scientific journals via its in-house developed scholarly publishing platform ARPHA.

As part of this new partnership, 20 journals published by Pensoft – including the publisher’s flagship titles ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal and Research Ideas and Outcomes (RIO Journal) amongst others – will now have their content automatically added to ResearchGate upon publication to benefit from enhanced visibility and discoverability through ResearchGate’s innovative Journal Home offering. These journals will all have dedicated profiles and be prominently represented on all associated article pages on ResearchGate, as well as all other relevant touch points throughout the network.

Journal Home provides a unique opportunity for Pensoft to connect its authors with their readers. The new journal profiles on ResearchGate will provide a central location for each journal, enabling researchers to learn more, discover new article content, and understand how, through their network, they are connected to the journal’s community of authors and editors. Authors of these journals additionally benefit from having their articles automatically added to their ResearchGate profile page, giving them access to metrics, including who is reading and citing their research. These rich insights will also enable Pensoft to build a deeper understanding of the communities engaging with its journals. 

“Pensoft is delighted to be working with ResearchGate to provide an even greater service to our authors and readers. ResearchGate offers an innovative way for us to grow the reach and visibility of our content, while also giving us a way to better understand and engage our author and reader audiences.”

said Prof Lyubomir Penev, CEO and founder of Pensoft.

“We couldn’t be happier to see Pensoft embark on this new partnership with ResearchGate. Journal Home will not only enable Pensoft authors to build visibility for their work, but provide them and Pensoft with greater insights about the communities engaging with that research. I look forward to seeing this new collaboration develop”

said Sören Hofmayer, co-founder and Chief Strategy Officer at ResearchGate.

About ResearchGate:

ResearchGate is the professional network for researchers. Over 25 million researchers use researchgate.net to share and discover research, build their networks, and advance their careers. Based in Berlin, ResearchGate was founded in 2008. Its mission is to connect the world of science and make research open to all.

Digitising UK Natural History Collections is vital to understand life on Earth, reports the Natural History Museum

In a paper published in the journal Research Ideas and Outcomes, authors estimate £18 million has been saved in efficiencies by researchers accessing digital specimens rather than physical collections.

· Scientists from the Natural History Museum (NHM) deep-dive into the uses and users of natural history collections held in the UK

· Modest estimates report a saving of £18 million in efficiencies by researchers accessing digital data rather than physical collections

· Today, software can complete in a week what it would take a human two years to achieve

· Call for investment to secure the UK’s stance as a world superpower in science and tech, and for a future in which both people and planet thrive

A new report has evaluated the use and impact of digitised natural science collections held in the UK and how they contribute to scientific, commercial and societal benefits.

UK natural science collections hold more than 137 million items spanning an incredible 4.56-billion-year history of life on Earth. These collections have emerged as a pivotal data resource to understanding the Earth in its past and current state – and will continue to inform the investors and policy-makers of the future.

UK natural science data in demand

GBIF—the Global Biodiversity Information Facility—is an international database providing open access data on all types of life on Earth. In this paper led by the NHM, scientists report that there are 7.6 million specimens, less than 6% of total UK natural science collections sampled, freely accessible on GBIF.

They found that 12% of the total peer-reviewed journal articles citing GBIF data specifically cite UK natural science collections. These data currently make up just 0.3% of total occurrences on GBIF, meaning they punch an incredible 40 times above their weight.

When asked previously, over 90% of GBIF users linked their use of these data to advancing the UN Sustainable Development Goals which look to reduce hunger, poverty and inequality, and spur economic growth while tackling climate change and protecting the oceans and forests.

The case for digitising UK natural science collections

The introduction of these collections onto a digital platform has revolutionised scientific research. In this paper published in the journal Research Ideas and Outcomes, the authors estimate £18 million has been saved in efficiencies by researchers accessing digital specimens rather than physical collections, assuming a minimal single physical visit replaced per citation. Of this, £1.4 million has been attributed to UK researchers, money which can be reinvested back into UK science institutions – those at the forefront of finding solutions to real world problems.

Lead author and Deputy Head of Digital, Data and Informatics, Helen Hardy says, ‘The advancement of digitisation has been truly transformational to the scientific community. Today it’s possible to use software that takes a week to achieve the type of information gathering it would take a human over 3,000 hours, or two years, to complete – individuals realising an entire life’s work in just a few months! Anticipation is high for further innovations such as the further integration of artificial intelligence into taxonomic work.’

UK government want the UK to be a science and technology superpower, and natural science collections provide a unique opportunity to achieve this. To unlock the true potential of collections data, UK Natural Science collections are joining forces through the Distributed System of Scientific Collections UK (DiSSCo) to make the case for investment of £155 million in a research infrastructure which is expected to unlock at least a seven- to ten- fold economic return on investment. Working alongside the Arts & Humanities Research Council (AHRC) and UK Research and Innovation (UKRI) to digitise the critical mass of collections, the data will be available through a robust technological infrastructure and continually developed in line with recent innovations.

Ken Norris, Deputy Director of Science at the NHM says, ‘In the midst of a planetary emergency, and what some experts believe to be the Earth’s sixth mass extinction event, estimates say that over 50% of the world’s GDP, which equates to approx. 44 trillion dollars, is dependent on the natural world. By understanding what is in collections now, both on a national and international scale, we can identify trends, necessary actions, and what we need to collect to underpin policy and investment decisions for a future where people and planet thrive.’

Hardy H, Livermore L, Kersey P, Norris K, Smith V, Pullar J (2023) Users and uses of UK Natural History Collections – a Summary, https://doi.org/10.5281/zenodo.8403318

A longer paper on this study including further detail on the methodology and findings is also available:

Hardy H, Livermore L, Kersey P, Norris K, Smith V (2023) Understanding the users and uses of UK Natural History Collections. Research Ideas and Outcomes 8: e113378 https://doi.org/10.3897/rio.9.e113378

Photo credit: Trustees of the Natural History Museum

Follow Research Ideas and Outcomes on Facebook, Twitter, and LinkedIn.

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.

***

Follow Pensoft on social media:

facebook
twitter

How it works: Nanopublications linked to articles in RIO Journal

To bridge the gap between authors and their readers or fellow researchers – whether humans or computers – Knowledge Pixels and Pensoft launched workflows to link scientific publications to nanopublications.

A new pilot project by Pensoft and Knowledge Pixels breaks scientific knowledge into FAIR and interlinked snippets of precise information

As you might have already heard, Knowledge Pixels: an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing by means of nanopublications – recently launched a pilot project with the similarly pioneering open-science journal Research Ideas and Outcomes (RIO), in a first of several upcoming collaborations between the software developer and the open-access scholarly publisher Pensoft.

“The way how science is performed has dramatically changed with digitalisation, the Internet, and the vast increase in data, but the results are still shared in basically the same form and language as 300 years ago: in narrative text, like a story. These narratives are not precise and not directly interpretable by machines, thereby not FAIR. Even the latest impressive AI tools like ChatGPT can only guess (and sometimes ‘hallucinate’) what the authors meant exactly and how the results compare,”

said Philipp von Essen and Tobias Kuhn, the two founders of Knowledge Pixels in a press announcement.

So, in order to bridge the gap between authors and their readers and fellow researchers – whether humans or computers – the partners launched several workflows to bi-directionally link scientific publications from RIO Journal to nanopublications. We will explain and demonstrate these workflows in a bit.

Now, first, let’s see what nanopublications are and how they contribute to scientific knowledge, researchers and scholarship as a whole.

What are nanopublications?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained by Knowledge Pixel on nanopub.net.

Basically, a nanopublication – unlike a research article – is just a tiny snippet of a scientific finding (e.g. medication X treats disease Y), which exists as a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. 

A nanopublication may also be an assertion related to an existing research article meant to support, comment, update or complement the reported findings.

In fact, nanopublications as a concept have been with us for quite a while now. Ever since the rise of the Semantic Web, to be exact. At the end of the day, it all boils down to providing easily accessible information that is only a click away from additional useful and relevant content. The thing is, technological advancement has only recently begun to catch up with the concept of nanopublications. Today, we are one step closer to another revolution in scientific publishing, thanks to the emergence and increasing adoption of what we call knowledge graphs.

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

said Prof. Lyubomir Penev, founder and CEO at Pensoft: the open-access scholarly publisher behind the very first semantically enhanced research article in the biodiversity domain, published back in 2010 in the ZooKeys journal.

Why nanopublications?

Apart from enabling computer algorithms with wholesome access to published research findings, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each byte of knowledge is interconnected and traceable back to its author(s) and scientific evidence. 

Nanopublications present a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels.

By granting computers the capability of exchanging information between users and platforms, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place. 

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.

By linking assertions to a publication by means of nanopublications allows the original authors and their fellow researchers to keep knowledge up to date as new findings emerge either in support or contradiction to previous information.

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. 

A scientific issue that would definitely benefit from an additional layer of provenance and, specifically, a workflow allowing for new updates to be linked to previous publications is the biodiversity domain, where species treatments, taxon names, biotic interactions and phylogenies are continuously being updated, reworked and even discarded for good. This is why an upcoming collaboration between Pensoft and Knowledge Pixels will also involve the Biodiversity Data Journal (stay tuned!)

What can you do in RIO?

Now, let’s have a look at the *nano* opportunities already available at RIO Journal.

The integration between RIO and Nanodash: the environment developed by Knowledge Pixels where users edit and publish their nanopublications is available at any article published in the journal. 

Add reaction to article

This function allows any reader to evaluate and record an opinion about any article using a simple template. The opinion is posted as a nanopublication displayed on the article page, bearing the timestamp and the name of the creator.

All one needs to do is go to a paper, locate the Nanopubs tab in the menu on the left and click on the Add reaction command to navigate to the Nanodash workspace accessible to anyone registered on ORCiD. 

To access the Nanodash workspace, where you can fill in a ready-to-use, partially filled in nanopublication template, simply go to the Nanopubs tab in the menu of any article published in RIO Journal and click Add reaction to this article (see example).

Within the simple Nanodash workspace, the user can provide the text of the nanopublication; define its relation to the linked paper using the Citation Typing Ontology (CiTO); update its provenance and add information (e.g. licence, extra creators) by inserting extra elements. 

To do this, the Knowledge Pixels team has created a ready-to-use nanopublication template, where the necessary details for the RIO paper and the author that secure the linkage have already been pre-filled.

Post an inline comment as a nanopublication

Another opportunity for readers and authors to add further meaningful information or feedback to an already published paper is by attaching an inline comment and then exporting it to Nanodash, so that it becomes a nanopublication. To do this, users will simply need to select some text with a left click, type in the comment, and click OK. Now, their input will be available in the Comment tab designed to host simple comments addressing the authors of the publication. 

While RIO has long been supporting features allowing for readers to publicly share comments and even CrossRef-registered post-publication peer reviews along the articles, the nanopublications integration adds to the versatile open science-driven arsenal of feedback tools. More precisely, the novel workflow is especially useful for comments that provide a particularly valuable contribution to a research topic.

To make a comment into a nanopublication the user needs to locate the comment in the tab, and click on the Post as Nanopub command to access the Nanodash environment.

Add a nanopublication while writing your manuscript

A functionality available from ARPHA Writing Tool – the online collaborative authoring environment that underpins the manuscript submission process at several journals published by Pensoft, including RIO Journal – allows for researchers to create a list of nanopublications within their manuscripts. 

By doing so, not only do authors get to highlight their key statements in a tabular view within a separate pre-designated Nanopublications section, but they also make it easier for reviewers and scientific editors to focus on and evaluate the very foundations of the paper.

By incorporating a machine algorithm-friendly structure for the main findings of their research paper, authors ensure that AI assistants, for example, will be more likely to correctly ‘read’, ‘interpret’ and deliver the knowledge reported in the publication for the next users and their prompts. Furthermore, fellow researchers who might want to cite the paper will also have an easier time citing the specific statement from within the cited source, so that their own readers – be it human, or AI – will make the right links and conclusions.

Within a pre-designated article template at RIO – regardless of the paper type selected – authors have the option to either paste a link to an already available nanopublication or manage their nanopublication via the Nanodash environment by following a link. Customised for the purposes of RIO, the Nanodash workspace will provide them with all the information needed to guide them through the creation and publication of their nanopublications.

Why Research Ideas and Outcomes, a.k.a. RIO Journal?

Why did Knowledge Pixels and Pensoft opt to run their joint pilot at no other journal within the Pensoft portfolio of open-access scientific journals but the Research Ideas and Outcomes (RIO)?

Well, one may argue that there simply was no better choice than an academic outlet that was initially designed to serve as “the open-science journal”: something it has been honourably recognised for by SPARC in 2016, only one year since its launch. 

Innovative since day #1, back in 2015, RIO surfaced as an academic outlet to publish a whole lot of article types, reporting on scientific work from across the research process, starting from research ideas, grant proposals and workshop reports. 

After all, back in 2015, when it was only a handful of funders who required Data and Software Management Plans to be made openly and publicly, RIO was already providing a platform to publish those as easily citable research outputs, complete with DOI and registration on Crossref. In the spirit of transparency, RIO has always operated an open and public by default peer review policy.

More recently, RIO introduced a novel collections workflow which allows, for example, project coordinators, to provide a one-stop access point for publications and all kinds of valuable outputs resulting from their projects regardless of their publication source.

Bottom line is, RIO has always stood for innovation, transparency, openness and FAIRness in scholarly publishing and communication, so it was indeed the best fit for the nanopublication pilot with Knowledge Pixels.

*** 

We encourage you to try the nanopublications workflow yourself by going to https://riojournal.com/articles, and posting your own assertion to an article of your choice!

Don’t forget to also sign up for the RIO Journal’s newsletter via the Email alert form on the journal’s website and follow it on Twitter, Facebook, Linkedin and Mastodon.