Category: Biodiversity Data Journal

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)

BiCIKL keeps on adding project outcomes in own collection in RIO Journal
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 ZooKeys, PhytoKeys, MycoKeys, Biodiversity 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.

Pensoft collaborates with R Discovery to elevate research discoverability

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

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

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

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

Lyubomir Penev

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

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

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

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

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

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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All good things come from above! DNA-based food analysis in the Leisler’s bat

Through the analysis of DNA traces in the droppings of a Leisler’s bat colony, researchers at LIB have now identified over 350 different insect species that were consumed by the bats.

Adequate food supply is a fundamental need and requirement for survival. To protect a species, it is often very helpful to know what that species prefers and frequently consumes. Through the analysis of DNA traces in the droppings of a Leisler’s bat colony, researchers at LIB (Leibniz Institute for the Analysis of Biodiversity Change) have now identified an astonishingly high number —over 350— different insect species that were consumed by the bats.

Portrait of the studied species Nyctalus leisleri, Leisler’s bat. © M. Koch

Especially for small animal species and those that are nocturnal, it can be extremely difficult to determine what they feed on. Identifying small prey insects or their remains is also rarely possible down to the exact species or family. In the case of the studied bat species, there is the additional challenge that it is a forest bat species that needs to be located first. “Following bats equipped with radio transmitters in the forest at night is quite special,” says Martin Koch, co-initiator of the study.

Design and installation of the guano trap (3 m) and roost entrance (9 m).

Fortunately — but also complicating matters — there are about 13 different bat species living in the investigated area near Bonn, in the forests of the Natura 2000 area ‘Waldreservat Kottenforst.’ Initially, as part of an EU Life+ project, roosts — the trees where the bats live — of the Leisler’s bats were identified, from which the study’s starting material was then obtained. This was done using a specially developed “guano trap.” The trap consists of approximately 2.2 square meters of mosquito netting stretched rectangularly.

It was installed about 3 meters high on the tree trunk, below the entrance to the roosting cavity at about 9 meters high. During the so-called “twilight swarming” after the nightly insect hunt, the bats return to the roosting cavity and initially circle the tree. They frequently perch briefly next to the cavity entrance and stick a small guano pellet to the trunk. Regularly, pellets fall and land in the mosquito netting under the cavity entrance. This “bat guano” was collected, fixed, and further processed in the laboratory.

“It’s fascinating how much DNA you can extract from a small amount of droppings and how much information we can draw from the DNA: from which bat species does the droppings come, and what has the bat eaten?” explains Dr. Kathrin Langen. Using the DNA contained in the droppings, our researchers were able to determine nine samples from nine different nights when only the target species swarmed around the roosting tree. On six other nights, other bats and a species of mouse were also active around the roosting tree. From the nine samples containing only the guano of the evening bat, an astonishingly rich menu was then reconstructed: the group consumed at least 126 different species of moths, 86 different species of flies and mosquitoes, 48 species of beetles, and a few dozen other various species of bugs, mayflies, caddisflies, and lacewings. Occasionally, spiders, harvestmen, lice, and other small animals were also consumed.

Timeline showing arthropod community composition at order level in the guano of N. leisleri, all three markers combined (COImldg, COIArt, 16S). With the exception of plots showing RRA assigned to major groups depending on sampling date (4C and 4F), read counts were not taken into account. A, D Number of species of each arthropod order detected at each time point; B, E Relative number of species per arthropod order as a percentage of the diet; C, F Species detected in each arthropod order, based on relative read abundances.

From the results, the team was able to deduce which of the three molecular genetic markers used worked best and provided the most species detections, a total of 358. “It’s incredibly satisfying to see what species lists come out at the end of all the lab work and bioinformatics,” says Dr. Sarah Bourlat, Head of the Metabarcoding Section at LIB, Bonn. However, the temporal course of the composition of the consumed insects was also interesting to observe: from late March to late June, the number of species in the guano steadily increases, only to decrease again by mid-August. This aligns very well with the activity patterns of certain insect groups.

The beech moth was the most frequently consumed butterfly, and a mayfly known as the transient virgin or ‘Uferaas’, was the most frequently consumed mayfly. The author team has listed the most important ecological parameters for the 18 key prey species in the study to contribute to better protecting the Leisler’s bat and the habitats needed by its prey insects.

Research article:
Bourlat SJ, Koch M, Kirse A, Langen K, Espeland M, Giebner H, Decher J, Ssymank A, Fonseca VG (2023) Metabarcoding dietary analysis in the insectivorous bat Nyctalus leisleri and implications for conservation. Biodiversity Data Journal 11: e111146. https://doi.org/10.3897/BDJ.11.e111146

News announcement originally published by the Leibniz Institute for the Analysis of Biodiversity Change. Republished with permission.

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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).”

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

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Entangled “her”stories – How to create an open multi-linked dynamic dataset of plant genera named for women

Which plant genera do you know that are named for women? Who were/are they?

Guest blog post by  Siobhan Leachman, Sabine von Mering, Heather Lindon & Carmen Ulloa Ulloa

How it all began

A post on social media asked about plant genera named for women and sparked a lively discussion with many contributors. This simple question was not as easily answered as initially thought. The resulting informal working group tackled this topic remotely during the COVID-19 pandemic and beyond. The team was motivated by the desire to amplify the contribution of women to botany through eponymy. The work of this team has so far resulted in a paper in Biodiversity Data Journal, presentations at several conferences, and a linked open dataset.

Prior to our international collaboration, no dataset was available to answer these simple questions and the required information was scattered in many different data sources. We set out to bring these data together and in doing so developed and refined our workflow. Our data paper documents this innovative workflow bringing together the various data elements needed to answer our research questions. Ultimately we created a Linked Open Data (LOD) dataset that amplified the names of women and female mythological beings celebrated through generic names of flowering plants.

Linking the Data

During our research process we focused on pulling data from a wide variety of sources while at the same time proactively sharing the data generated as widely as possible. This was done by adding and linking it to multiple public databases and sources (push-pull) including the International Plant Name Index (hereafter IPNI), Tropicos®, Wikidata, Bionomia and the Biodiversity Heritage Library (hereafter BHL).

Visualisation of our workflow to create a working list of flowering plant genera named for women. 

For our list of genera, each of the protologues were reviewed to confirm the etymology or eponymy. To find the generic prologues, we searched botanical databases such as IPNI and Tropicos, openly accessible providers of digital publications and other digital libraries and websites that provide free access to such publications. Here the BHL was invaluable as the majority of protologues and many other relevant publications were openly accessible through this digital library. Where no digital publication was available we accessed scientific literature through our affiliated institutions.

For the women, our starting point was the “Index of Eponymic Plant Names – Extended Edition” by Lotte Burkhardt (2018). We manually extracted all genera honouring women.  This dataset was supplemented with other sources including IPNI (2023), Mari Mut (2017-2021), a 2022 updated version of Burkhardt’s document (Burkhardt 2022), as well as suggestions received from colleagues and generated from our own research.

We collected the following information as structured data: information on the woman honoured, the genera named in honour of the woman, the year and place of the protologue or original publication (the nomenclatural reference), the author(s) of the genus name, and the link to the protologue or original publication if available online.

Wikidata

Wikidata was the central data repository and linking mechanism for this project as it provided structured data that can be read and edited by humans and machines and it acts as a hub for other identifiers. As such Wikidata played a central role in semantic linking and enriching of our data.

Wikidata items for the plant genera were created or enriched with information about the name, the author(s) of the genus and the year of publication. Those statements were referenced using the original publication. If the protologue was available on BHL, the BHL bibliographic or page number was added to that reference, thus creating a digital link improving access to the protologue. While undertaking this work we also collated a list of all those public domain publications that appeared to be absent from BHL. We passed on this list to BHL and requested these texts be scanned and added to BHL for the benefit of everyone.

We then added a named after statement to the Wikidata item for the appropriate plant genera linking that item to the Wikidata item for the woman honoured. Wikidata items for the women honoured were newly created or enriched. We researched each person and her contributions, plus information on mythological figures where necessary, and added this information to Wikidata items. Our work also included disambiguating the woman from other people with identical or similar names. 

To amplify the women’s contributions to science and to enrich the wider (biodiversity) data ecosystem, we linked to other Wikidata items and websites or databases by adding other relevant identifiers. For example if the women were botanists, botanical collectors or other naturalists, we used the author property to link the women to publications written by them. In addition, we added the women to Bionomia and attributed specimens collected or identified by them to their profiles.

Our work also included enriching Wikidata items of taxon authors. IPNI and Tropicos were searched for these author names, and websites such as BHL, the Global Biodiversity Information Facility (GBIF) or other specialist databases were consulted. Corrections or newly researched information on taxon authors was placed not just in Wikidata but was also sent together with the corresponding references to IPNI and Tropicos. This information was then used by those organizations to update these databases accordingly. 

As a result of our data being placed in Wikidata it is available to be queried via the Wikidata Query Service.  

Our Goal Achieved

As a result of our project, we published a dataset of 728 genera honouring women or female beings. This was a nearly twenty-fold increase in the number of genera linked to women in Wikidata. Our analysis paper on this data is forthcoming.

Notable Women 

Monsonia L.

All of us came away from this research with a favourite story. One that stood out was Ann Monson, for whom Linnaeus named Monsonia. Linnaeus wrote a delightful letter to her about their creating, platonically of course, a kind of plant love-child between them, in the form of this new genus.

Translated from Latin : “….Lock these [seeds] in a pot, and place them in the window of the chamber towards the sun, when it bursts forth in February, and in the first summer the sun blooms and lasts the most beautiful Alstromeria, which no one has seen in England, and you bring forth no flowers. If it should come to pass, as I wish, if you offer our flames, I would only wish to beget with you an only child, as a pledge of my love, little Monsonia, by which you may perpetuate the fame of Lady in the kingdom of Flora, who was the Queen of Women.”

Fittonia Coem.

Two eponymous women with an interesting story are Sarah Mary Fitton and her sister Elizabeth. They wrote Conversations on Botany in 1817 accompanied by colour engravings of flowers which popularised botany with women. The genus Fittonia was named in their honour.

Chanekia Lundell

Another woman honoured in a plant genus was Mercedes Chanek, a Mayan plant collector who worked in the 1930’s for Cyrus Longworth Lundell and collected for the University of Michigan in British Honduras, today Belize. Very little is known about her life and work. However, her collections are detailed in Tropicos and Bionomia, and you can see the genus named for her by Lundell in IPNI under Chanekia.

Medusa Lour. and other genera

Medusa (c. 1597), by Caravaggio

An example of a mythological female being honoured in several plant names is that of Medusa, who has the most genera named after her, six, more than any real woman!

We hope that our data paper inspires others to use the methodology and workflow described to create other linked open datasets, e.g. celebrating and amplifying the contributions of underrepresented or marginalised groups in science.

Data paper: 

von Mering S, Gardiner LM, Knapp S, Lindon H, Leachman S, Ulloa Ulloa C, Vincent S, Vorontsova MS (2023) Creating a multi-linked dynamic dataset: a case study of plant genera named for women. Biodiversity Data Journal 11: e114408. https://doi.org/10.3897/BDJ.11.e114408

A new dawn for biological collections: The AI revolution in museums and herbaria

There are numerous uses for machine learning in digital collections, including an enormous potential to extract traits of organisms.

Guest blog post by Quentin Groom

Imagine having access to all the two billion biological collections of the world from your desktop! Not only to browse, but to search with artificial intelligence. We recently published a paper where we envisage what might be possible, such as searching all specimen labels for a person’s signature, studying the patterns of butterflies’ wings, or reconstructing a historic expedition.

Numbers of digital images from biodiversity collections are increasing exponentially. Herbariums have led the way with tens of millions of images available, but images of pinned insects will soon overtake plants.

Numbers of accessible images of specimens are increasing exponentially. Plants lead the way, but insects are increasing at the fastest rate. This graph was created from snapshots of the Global Biodiversity Information Facility and is undoubtedly an underestimate of the actual number of specimens for which images exist. See how this was created in Groom et al. (2023).

At one time, if you wanted access to biological collections, you had to travel. Now we are used to visiting collections online, where we can view images of specimens and their details on our desktops. Nevertheless, biological collection images are still dispersed and this limits their effective use, not just for people, but also for computers. One of the promises of making specimens digital is being able to apply machine learning to these images.  Yet the real benefits of machine access to specimens can only be realised through massive access to collection images and the ability to apply these techniques to hundreds of collections and millions of specimens.

Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude.

In our paper in Biodiversity Data Journal, we examined some of the numerous uses for machine learning in digital collections. These include an enormous potential to extract traits of organisms, from the size and shape of different organs, to their colours, patterns, and phenology. Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude. We would not only be able to study the intricacies of evolution, but also practical subjects, such as the mechanics of pollination in insects, adaptations to drought in plants, and adaptations to weediness in invasive species.

Machine access to these images will also provide an unparalleled view of the history of the biological sciences, the specimens used to describe species, the evidence for evolution, the people involved and institutions that contributed. Such transparency may reveal some amazing stories of scientific exploration, but will undoubtedly also shed light on some of the less exemplary actions of colonialism. Yet if we are to redress the injustices of the past we need to have a balanced view of collections, and we should do this openly.

Specimen labels provide numerous clues to their history often in the form of stamps and emblems. A BR0000013433048 Meise Botanic Garden (CC-BY-SA 4.0). B USCH0030719, A.C. Moore Herbarium at the University of South Carolina (public domain). C E00809288, Royal Botanic Garden Edinburgh (public domain). D USCH0030719, University of South Carolina (public domain). E E00919066, Royal Botanic Garden Edinburgh (public domain). F BR0000017682725, Meise Botanic Garden (CC-BY-SA 4.0). G P00605317, Museum National d’Histoire Naturelle, Paris (CC-BY 4.0). H LISC036829, Instituto de Investigação Científica Tropical (CC-BY-NC 4.0). l PC0702930, Muséum National d’Histoire Naturelle, Paris (CC-By 4.0). J same specimen as (B). K PC0702930 Muséum National d’Histoire Naturelle, Paris (CC-BY 4.0). L 101178648, Missouri Botanical Garden (CC-BY-SA 4.0).

With such unparalleled access to collections, we could travel vicariously to times and places that are hard to reach in any other way. Fieldwork is expensive and time-consuming, and can’t provide the historic perspective of collections, let alone the geographic extent. Furthermore, digital resources have the potential to democratise collections, allowing anyone the opportunity to study these collections irrespective of location.

Is such a vision of integrated digital collections possible? It certainly is! The technologies already exist, not just for machine learning, but also to create the infrastructure to provide access to millions of digital images and their metadata. Initiatives, such as DiSSCo in Europe and iDigBio in the USA are moving in this direction. Yet, we conclude that the main challenge to realising this vision of the future is a sociopolitical one. Can so many institutions and funders work together to pool their resources? Can collections in rich countries share the sovereignty of their collections with the countries where many of the specimens originated?

If you too share the dream, we encourage you to support or contribute to initiatives working in this direction, whether through funding, collaboration, or sharing knowledge. If the full potential of digital collections is to be realised, we need to think big and work together.

Research article:

Groom Q, Dillen M, Addink W, Ariño AHH, Bölling C, Bonnet P, Cecchi L, Ellwood ER, Figueira R, Gagnier P-Y, Grace OM, Güntsch A, Hardy H, Huybrechts P, Hyam R, Joly AAJ, Kommineni VK, Larridon I, Livermore L, Lopes RJ, Meeus S, Miller JA, Milleville K, Panda R, Pignal M, Poelen J, Ristevski B, Robertson T, Rufino AC, Santos J, Schermer M, Scott B, Seltmann KC, Teixeira H, Trekels M, Gaikwad J (2023) Envisaging a global infrastructure to exploit the potential of digitised collections. Biodiversity Data Journal 11: e109439. https://doi.org/10.3897/BDJ.11.e109439

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.