Pensoft launches official Weibo account to expand global reach

The Pensoft team is looking forward to engaging in conversations with its Chinese authors, editors, and readers.

Scholarly publisher Pensoft is excited to announce it is now on Chinese social media platform Weibo. The move is aimed at fostering stronger connections with researchers, academics, and enthusiasts in China, which in turn will enhance the dissemination of scientific knowledge and facilitate international collaboration.

With over half a billion active users, Weibo is a powerful social media platform that combines the functionalities of microblogging and social networking. The Pensoft team is looking forward to engaging in real-time conversations with its Chinese audience, sharing insights, and receiving their feedback.

The launch coincides with the Dragon Boat Festival, a significant cultural event in China that commemorates the ancient poet Qu Yuan and symbolizes unity and teamwork. 

The move aims to make Pensoft’s publications and updates more accessible to Chinese researchers, allowing them to stay informed about the latest scientific discoveries and advancements. In addition, it offers an excellent opportunity for Pensoft to foster collaborations with Chinese institutions, researchers, and academic societies.

As a pioneer in open-access publishing, Pensoft will also use its Weibo account to promote the benefits of open access, making sure Chinese research reaches a global audience without paywalls.

“China, with its rapidly growing research output and a burgeoning community of scholars, represents a significant segment of the global academic landscape. Recognizing the importance of engaging with this vibrant community, Pensoft’s decision to establish a presence on Weibo underscores its commitment to inclusivity and accessibility in scientific publishing,” says Lyubomir Penev, CEO and founder of Pensoft.

We invite you to join Pensoft’s Weibo account to learn all about our latest scientific discoveries and publishing updates.

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.

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.

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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.

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/ 

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

On multiple occasions, the participants agreed that the Biodiversity Knowledge Hub must be the flagship outcome of BiCIKL. 

The city of Cambridge and the Wellcome Campus hosted the Final General Assembly of the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library): a 36-month endeavour that 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. Consortium members who could not attend the meeting in Cambridge joined the meeting remotely.

The 3-day meeting was organised by local hosts European Molecular Biology Laboratory (EMBL) and ELIXIR in collaboration with Pensoft Publishers.

After a welcome cocktail reception on Monday evening at Hilton Cambridge City Centre, on Tuesday, the consortium made an early start with a recap of BiCIKL’s key milestones and outputs from the last three years. All Work Package leaders had their own timeslot to discuss the results of their collaborations.  

They all agreed that the Biodiversity Knowledge Hub – the one-stop portal for understanding the complex – yet increasingly interconnected landscape of biodiversity research infrastructures – is likely the flagship outcome of BiCIKL. 

Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers at the BiCIKL’s third and final General Assembly in Cambridge, United Kingdom.

In the afternoon, the participants focused on the services developed under BiCIKL. Amongst the many services resulting from the project some were not originally planned. Rather those were the ‘natural’ products of the dialogue and collaboration that flourished within the consortium throughout the project. “A symptom of passion,” said Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers.

An excellent example of one such service is what the partners call the “Biodiversity PMC”, which brings together biodiversity literature from thousands of scholarly journals and over 500,000 taxonomic treatments, in addition to the biomedical content available from NIH’s PubMed Central, into the SIB Literature Services (SIBiLS) database. What’s more, users at SIBiLS – be it human or AI – can now use advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions. Read more about the “Biodiversity PMC” in its recent official announcement.

Far from being the only one, the “Biodiversity PMC” is in good company: from the blockchain-based technology of LifeBlock to the curation of the DNA sequences by PlutoF, the BiCIKL project consortium takes pride in having developed twelve services dedicated to FAIR and linked ready-to-use biodiversity data. 

All those services are already listed in the FAIR Data Place within the Biodiversity Knowledge Hub, where each is presented with its own video. For many services, from the same page, visitors can also download factsheets meant to serve as user guidelines. All will also be featured in the EOSC catalogue.

All services developed under BiCIKL with links to their explanatory videos:

On Wednesday, the consortium focused on BiCIKL’s activities from the Transnational and Virtual Access Pillar, which included both presentations by each open call leader and VA leader, as well as open discussions and a recap of what the teams have learnt from these experiences. 

A panel discussion took place on Thursday as part of an open event, where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus.

Thursday was dedicated to an open event where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus. You can find the agenda on BiCIKL’s website.

After 36 months of action, the BiCIKL project will officially end in April 2024, but does it mean that all will be done and dusted come May 2024? Certainly not, point out the partners. 

To ensure that the Biodiversity Knowledge Hub will not only continue to exist but will not cease to grow in both use and participation, the one-stop portal will remain under the maintenance of LifeWatch ERIC. 

In conclusion, we could say that an appropriate payoff for the project is “Stick together!” as put by BiCIKL’s Joint Research Activity Leader Dr. Quentin Groom.

Final words at the third and last General Assembly of the BiCIKL project.

You can find highlights from the BiCIKL General Assembly meeting on X via the #BiCIKL_H2020 hashtag (in association with #Cambridge and #finalGA)

All research outputs, including the approved grant proposal, policy briefs, guidelines papers and research articles associated with the project, remain openly accessible from the BiCIKL project outcomes collection in RIO Journal: https://doi.org/10.3897/rio.coll.105.

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All BiCIKL project partners:

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

The indexing is one of the major outcomes from the partnerships within the Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL)

Amongst the major outcomes from the currently nearly completed Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL) – dedicated to making biodiversity data FAIR and bi-directionally linked – brings the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

In a joint effort between the Swiss-based Text Mining group of Patrick Ruch at SIB (developing SIBiLS), the text- and data-mining association Plazi and scientific publisher Pensoft, the long-time collaborators have started feeding full-text content of over 500,000 taxonomic treatments extracted by Plazi and tens of thousands full-text articles from 40 well-renowned biodiversity journals published by Pensoft to the SIBiLS database. 

What this means is that users at SIBiLS – be it human or AI – have now gained access to advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions.

To index and directly feed the content from its 40+ academic outlets at SIBiLS, Pensoft relies on advanced and full-text TaxPub JATS XML journal publication workflow, powered by the ARPHA publishing platform. Meanwhile, Plazi uses its GoldenGate text- and data-mining software to harvest taxon treatments from over 80 journals stored at TreatmentBank and the Biodiversity Literature Repository, and then further re-used by GBIF, OpenBiodiv and now by SiBILS.

Seen as a pilot, the indexing – the partners believe – could soon be extended with other journals relying on modern publishing or converted legacy publications. 

In fact, ever since its launch in 2020, the queryable database SIBiLS has been retrieving relevant full-text papers directly from the NIH’s PubMed Central, including Pensoft’s ZooKeysPhytoKeysMycoKeysBiodiversity Data Journal and Comparative Cytogenetics

However, there were still gaps left to bridge before SIBiLS could indeed be dubbed “the Biodiversity PMC”, and those have mostly been about volume and breadth of content. While the above-mentioned five journals by Pensoft had long been indexed by SIBiLS through harvesting PMC, those had been quite an exception since, several years ago, a reorganisation at PMC moved the focus of the database to almost exclusively biomedical content, thus leaving biodiversity journals out of the scope of the database.

In the meantime, while Plazi has been feeding SIBiLS a growing volume of taxonomic treatments and visual data, as it was exponentially increasing the number of publishers and journals it mined data from, a lot of biodiversity data (e.g. genetic, molecular, ecological) published in the article narratives that were not taxon treatments could not make it to the portal.

“We all know the advantages and practical uses PMC offers to its users, so we cannot miss the opportunity to incorporate this well-proven approach to navigate the data deluge in biodiversity science. Undoubtedly, it is an extremely ambitious and demanding task. Yet, I believe that, at the BiCIKL consortium, we have made it pretty clear we have the necessary expertise, know-how and aspiration to take on the challenge,”

said Prof. Lyubomir Penev, founder/CEO at Pensoft and project coordinator of BiCIKL.

“For far too long, scientific knowledge about biodiversity has been imprisoned in a continuously growing corpus of scientific outputs, which – most of the time – are published in unstructured formats, such as PDF, or as paywalled content, and often locked by both! This means that they are – at best – difficult to access and comprehend by computer algorithms. In the meantime, we need all that knowledge, in order to accelerate our understanding of the dynamics of the global biodiversity crisis and to efficiently assess the impact of climate change. This is why the need for advanced workflows and tools to annotate, mine, query and discover new facts from the available literature is more than obvious,”

added Dr. Donat Agosti, President at Plazi.

“In the course of the BiCIKL project, at SIBiLS, we started indexing a larger set of biodiversity-related contents in the broad sense, including environmental sciences and ecology, to build a new literature database, or what we now call ‘Biodiversity PMC’. Now, with the help of Plazi and Pensoft, we provide a unique entry point to half a million taxonomic treatments, which were not included into the original PubMed Central. Next on the list is to expand our network of literature sources and continue this exponential growth of queryable biodiversity knowledge to turn Biodiversity PMC into the “One Health” library. We promise to keep you posted,”

said Dr. Patrick Ruch, Group Leader at SIB and Head of Research at HES-SO, HEG Geneva, Switzerland. 

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Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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About the SIB Swiss Institute of Bioinformatics:

SIB is an internationally recognized non-profit organisation, dedicated to biological and biomedical data science. SIB’s data scientists are passionate about creating knowledge and solving complex questions in many fields, from biodiversity and evolution to medicine. They provide essential databases and software platforms as well as bioinformatics expertise and services to academic, clinical, and industry groups. With the recent creation of the Environmental Bioinformatics group, led by Robert Waterhouse, SIB is engaged in an unprecedented effort to streamline data across molecular biology, health and biodiversity. SIB also federates the Swiss bioinformatics community of some 900 scientists, encouraging collaboration and knowledge sharing.

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About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; is co-founder of the Biodiversity Literature Repository at Zenodo, participates in the development of new models for publishing taxonomic treatments in order to maximise interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data. Plazi is a major contributor to the Global Biodiversity Information Facility.

Celebrating scientific excellence: Dr. Paul D. N. Hebert awarded the Benjamin Franklin Medal

Dr. Paul D. N. Hebert, known as “the father of DNA barcoding,” has been honoured with the prestigious Benjamin Franklin Medal, a testament to his trailblazing contributions to biodiversity science.

Dr. Paul D. N. Hebert. Photo credit Åge Hojem, NTNU Vitenskapsmuseet/NTNU University Museum, used under a CC BY 2.0 licence

Dr. Hebert’s innovative work has advanced our understanding of global biodiversity, making the identification of species easier, which in turn helps support global conservation efforts. By devising a method that allows the quick and efficient discerning of species, he has transformed biodiversity science.

DNA barcoding has many applications in the classification and monitoring of biodiversity. It can help protect endangered species, control agriculture pests, and identify disease vectors.

Founder and Director of the Centre for Biodiversity Genomics and Chief Executive Officer of the International Barcode of Life consortium (iBOL), Dr. Hebert is one of the leading voices of today’s biodiversity innovation and research.

Dr. Hebert is also chair of the advisory board of Pensoft’s journal Metabarcoding and Metagenomics. He has authored 13 papers in ZooKeys, substantially contributing to untangling the taxonomy of braconid wasps, butterflies, and other insects.

Acylomus ergoti, one of the many insect species Dr. Hebert has worked on.

His work has also appeared in other Pensoft-published journals, such as Biodiversity Data Journal, Nota Lepidopterologica, and Deutsche Entomologische Zeitschrift.

His innovative approach has sparked discussions and debates around the role of novel methodologies in taxonomy.

Dr. Hebert’s recognition with the Benjamin Franklin Medal demonstrates the critical role of biodiversity studies in dealing with global challenges such as the biodiversity crisis. He has inspired a generation of scientists to push the boundaries of knowledge and drive innovation in research technology.

We at Pensoft extend our heartfelt congratulations to Dr. Paul D. N. Hebert on this well-deserved recognition. He continues to lead the way in unravelling the complexities of global biodiversity.

Pensoft 2023 review: A year of pioneering research

To celebrate a successful year, Pensoft gives thanks and reflects on the achievements of key journals in 2023.

As the new year approaches, we take a moment to look back on a great year for several of Pensoft‘s key journals.

The following videos were created as part of the #Pensoft2023Review campaign and present the journals’ achievements this year.

ZooKeys

PhytoKeys

MycoKeys

Biodiversity Data Journal

NeoBiota

Nature Conservation

One Ecosystem

Metabarcoding and Metagenomics

Evolutionary Systematics

Looking forward to 2024

Despite the success of 2023, the Pensoft team is keener than ever to improve in every aspect in the coming year. A massive thank you to every author, editor, reviewer and reader of Pensoft’s journals, and a very happy New Year!

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Conferences across the continents: Pensoft’s events in Autumn 2023

Pensoft participated in several events all around the world in October and November 2023.

October and November 2023 were active months for the Pensoft team, who represented the publisher’s journals and projects at conferences in Europe, North America, South America, Oceania and Asia.

Let’s take a look back at all the events of the past two months.

The Biodiversity Information Standards Conference 2023

The Biodiversity Information Standards (TDWG) Conference, held from October 9-13 in Tasmania, Australia, brought together experts and stakeholders from the global biodiversity research community.

The annual gathering is a crucial platform for sharing insights, innovations, and knowledge related to biodiversity data standards and practices. Key figures from Pensoft took part in the event, presenting new ways to improve the management, accessibility, and usability of biodiversity data. 

Prof. Lyubomir Penev, founder and Chief Executive Officer of Pensoft, gave two talks that highlighted the importance of data publishing. His presentation on “The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data” underscored the significance of FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. BKH is the major output from the Horizon 2020 project BiCIKL (Biodiversity Community Integrated Knowledge Library) dedicated to linked and FAIR data in biodiversity, and coordinated by Pensoft.

Prof. Lyubomir Penev, Pensoft founder and CEO.

He also introduced the Nanopublications for Biodiversity workflow and format: a promising new tool developed by Knowledge Pixels and Pensoft to communicate key scientific statements in a way that is human-readable, machine-actionable, and in line with FAIR principles. Earlier this year, Biodiversity Data Journal integrated nanopublications into its workflow to allow authors to share their findings even more efficiently.

Chief Technology Officer of Pensoft Teodor Georgiev contributed to the conference by presenting “OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph.” His session highlighted the innovative approaches being taken to explore and leverage a biodiversity knowledge graph, showcasing the importance of technology in advancing biodiversity research.

Teodor Georgiev (right), Pensoft CTO.

Many authors and editors at Biodiversity Data Journal also spoke at the TDWG conference, including Vince Smith, the journal’s editor-in-chief, who is Head of Digital, Data, and Informatics at the Natural History Museum. He delivered insightful presentations on digitising natural science collections and utilising AI for insect collections.

GEO BON Global Conference 2023

GEO BON’s Global Conference on Biodiversity and Monitoring took place from 10-13 October 2023 in Montreal, Canada.

Metabarcoding and Metagenomics editor-in-chief, Florian Leese.

The theme of the conference was “Monitoring Biodiversity for Action” and there was particular emphasis on the development of best practices and new technologies for biodiversity observations and monitoring to support transformative policy and conservation action.

Metabarcoding & Metagenomics’ editor-in-chief, Florian Leese, was one of the organisers of the “Standardized eDNA-Based Biodiversity Monitoring to Inform Environmental Stewardship Programs” session. Furthermore, the journal was represented at Pensoft’s exhibition booth, where conference participants were able to discuss metabarcoding and metagenomics research.

Following the conference, Metabarcoding & Metagenomics announced a new special issue titled “Towards Standardized Molecular Biodiversity Monitoring.” The special issue is accepting submissions until 15th March 2024.

Asian Mycological Congress 2023

The Asian Mycological Congress welcomed researchers from around the world to Busan, Republic of Korea, for an exploration of all things fungi from 10-13 October. 

MycoKeys Best Talk award (winner not pictured).

Titled “Fungal World and Its Bioexploitation – in all areas of basic and applied mycology,” the conference covered a range of topics related to all theoretical and practical aspects of mycology. There was a particular emphasis on the development of mycology through various activities associated with mycological education, training, research, and service in countries and regions within Asia.

As one of the sponsors of the congress, Pensoft proudly presented a Best Talk award to Dr Sinang Hongsanan of Chiang Mai University, Thailand. The award entitles the winner to a free publication in Pensoft’s flagship mycology journal, MycoKeys.

Joint ESENIAS and DIAS Scientific Conference 2023

The ESENIAS and DIAS conference took place from 11-14 October and focused on “globalisation and invasive alien species in the Black Sea and Mediterranean regions.” Pensoft shared information on their NeoBiota journal and the important REST-COAST and B-Cubed projects.

Polina Nikova receiving the NeoBiota Best Talk Award.

Polina Nikova of the Bulgarian Academy of Sciences received the NeoBiota Best Talk Award for her presentation titled “First documented records in the wild of American mink (Neogale vision von Schreber, 1776) in Bulgaria.” The award entitles her to a free publication in the NeoBiota journal.

XII European Congress of Entomology

Pensoft took part in the XII European Congress of Entomology (ECE 2023) in Heraklion, Crete, from 16-20 October. The event provided a forum for entomologists from all over the world, bringing together over 900 scientists from 60 countries.

Carla Stoyanova, Teodor Metodiev and Boriana Ovcharova representing Pensoft.

The ECE 2023, organised by the Hellenic Entomological Society, addressed the pressing challenges facing entomology, including climate change, vector-borne diseases, biodiversity loss, and the need to sustainably feed a growing world population. The program featured symposia, lectures, poster sessions, and other types of activities aimed at fostering innovation in entomology. For Pensoft, they were a great opportunity to interact with scientists and share their commitment to advancing entomological research and addressing the critical challenges in the field.

Throughout the event, conference participants could find Pensoft’s team at thir booth, and learn more about the scholarly publisher’s open-access journals in entomology. In addition, the Pensoft team presented the latest outcomes from the Horizon 2020 projects B-GOOD, Safeguard, and PoshBee, where the publisher takes care of science communication and dissemination as a partner.

XIV International Congress of Orthopterology 2023

The XIV International Congress of Orthopterology, held from 16-19 October in Mérida, Yucatán, México, was a landmark event in the field of orthopterology.

Group photo of XIV International Congress of Orthopterology 2023 participants.

Hosted for the first time in Mexico, it attracted experts and enthusiasts from around the world. The congress featured plenary speakers who presented cutting-edge research and insights on various aspects of grasshoppers, crickets, and related insects.

Pensoft’s Journal of Orthoptera Research was represented by Tony Robillard, the editor-in-chief, who presented the latest developments of the journal to attendees.

Symposia, workshops, and meetings facilitated discussions on topics like climate change impacts, conservation, and management of Orthoptera. The event also included introductions to new digital and geospatial tools for Orthoptera research.

The 16th International Conference on Ecology and Management of Alien Plant Invasions

The 16th International Conference on Ecology and Management of Alien Plant Invasions (EMAPI 2023) took place in Pucón, Chile, from 23-25 October . The conference focused on the promotion of diversity in the science and management of biological invasions. Several NeoBiota authors ran sessions at the conference, and the journal also presented a Best Talk Award.

4th International ESP Latin America and Caribbean Conference

The 4th International ESP Latin America and Caribbean Conference (ESP LAC 2023) was held in La Serena, Chile, from 6-10 November. Focused on “Sharing knowledge about ecosystem services and natural capital to build a sustainable future,” the event attracted experts in ecosystem services, particularly from Latin America and the Caribbean.

Organised by the Ecosystem Services Partnership, this bi-annual conference was open to both ESP members and non-members, featuring a hybrid format in English and Spanish. Attendees enjoyed an excursion to La Serena’s historical center, adding a cultural dimension to the event.

The conference included diverse sessions and a special recognition by Pensoft’s One Ecosystem journal, which awarded full waivers for publication to the authors of the three best posters.

Magaly Aldave receiving the Best Poster Award.

Magaly Aldave of the Transdisciplinary Center for FES-Systemic Studies claimed first prize with “The voice of children in the conservation of the urban wetland and Ramsar Site Pantanos de Villa in Metropolitan Lima, Peru.” Ana Catalina Copier Guerrero and Gabriela Mallea-Rebolledo, both of the University of Chile, were awarded second and third prize respectively.

Biosystematics 2023

Biosystematics 2023, held from 26-30 November at the Australian National University in Canberra, was a collaborative effort of the Australian Biological Resources Study, Society of Australian Systematic Biologists, Australasian Mycological Society, and Australasian Systematic Botany Society. Themed “Celebrating the Past | Planning the Future,” the conference provided a platform for exploring advancements in biosystematics.

The event featured in-person and online participation, catering to a wide audience of researchers, academics, and students. It included workshops, presentations, and discussions, with a focus on enhancing understanding in biosystematics.

Pensoft awarded three student prizes at the event. Putter Tiatragu, Australian National University, received the Best Student Talk award and a free publication in any Pensoft journal for “A big burst of blindsnakes: Phylogenomics and historical biogeography of Australia’s most species-rich snake genus.”

Helen Armstrong, Murdoch University, received the Best Student Lightning Talk for “An enigmatic snapper parasite (Trematoda: Cryptogonimidae) found in an unexpected host.” Patricia Chan, University of Wisconsin-Madison, was the Best Student Lightning Talk runner-up for “Drivers of Diversity of Darwinia’s Common Scents and Inflorescences with Style: Phylogenomics, Pollination Biology, and Floral Chemical Ecology of Western Australian Darwinia (Myrtaceae).”

As we approach the end of 2023, Pensoft looks back on its most prolific and meaningful year of conferences and events. Thank you to everyone who contributed to or engaged with Pensoft’s open-access journals, and here’s to another year of attending events, rewarding important research, and connecting with the scientific community.

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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.

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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