Beneath the arid pre-Saharan zone of Morocco lies Aziza Cave, also known as Kef Aziza or Tazouguert Cave. The vast subterranean system stretches over 3.5 kilometers of surveyed galleries, making it Morocco’s fifth-largest cave system and one of the top ten most extensive caves in North Africa.
A view of the Sahara desert and Aziza cave’s entrance.
Beyond its sheer size and geological significance, Aziza Cave harbors a rich and diverse array of subterranean life that is only now beginning to be revealed widely. In a recent study in the journal Subterranean Biology, researchers cataloged the subterranean fauna of Aziza Cave and provided a detailed checklist of 26 different taxa potentially representing cave-restricted species. Among these are 22 troglobitic species, organisms that have adapted to life entirely within the cave environment, and four stygobitic species, which have specially evolved to live in the cave’s groundwater.
Four of the authors of the paper.
The discovery of such a variety of species highlights the cave as a critical biodiversity hotspot, not only in Morocco but for the African continent as a whole. One alarming aspect of this discovery is the large number of species that still need to be thoroughly studied or described.
Dysdera caeca, a cave spider
Only about 34.6% of the species in Aziza Cave have been formally identified and described by scientists. Further research could lead to the identification and description of many new species. The fauna found in Aziza Cave includes a wide variety of life forms, with the richest groups being beetles (Coleoptera), spiders (Araneae), springtails (Entomobryomorpha), and woodlice (Isopoda). Some have evolved remarkable adaptations to their lightless, nutrient-scarce environment, such as reduced pigmentation, elongated appendages, and heightened sensory capabilities that help them navigate and survive in this extreme habitat.
Long-tailed bat Rhinopoma hardwickei.
Despite these discoveries, much of Aziza Cave remains unexplored. Large portions of this karstic system have yet to be surveyed, and researchers believe that the biodiversity uncovered so far is just the beginning. The cave’s unexplored depths likely hold many more secrets, including potentially new species that have yet to be seen by human eyes. This prospect has sparked great interest among speleologists and conservationists, who see Aziza Cave as an important research site for studying subterranean ecosystems.
Magnezia gardei, a cave isopod.
The biodiversity of Aziza Cave is something to celebrate, but it also sheds light on the significant conservation challenges that subterranean habitats in Morocco and across North Africa are facing. Caves are delicate ecosystems that are highly sensitive to changes in their environment. Human activities such as pollution, mining, deforestation, and unsustainable tourism pose severe threats to these ecosystems and the species that depend on them. Once these habitats are damaged or destroyed, it is often impossible to restore them, and the species that inhabit them may face extinction.
Graffiti on the cave walls.
Human-induced impacts have already begun to take their toll in Aziza Cave. Visitors can disrupt the delicate balance of the cave’s ecosystem, change water quality, or introduce pollutants and alien species. These pressures underscore the urgent need for conservation measures to protect this unique environment and its inhabitants. By highlighting the importance of Aziza Cave and similar habitats, the researchers hope to encourage further exploration and study of Africa’s subterranean ecosystems and develop effective conservation strategies to protect them. By protecting these fragile ecosystems and supporting scientific exploration, we can ensure that the incredible biodiversity of Aziza Cave and other subterranean habitats continues to thrive.
Research article:
Moutaouakil S, Souza-Silva M, Oliveira LF, Ghamizi M, Ferreira RL (2024) A cave with remarkably high subterranean diversity in Africa and its significance for biodiversity conservation. Subterranean Biology 50: 1-28. https://doi.org/10.3897/subtbiol.50.113919
Guest blog post by Petra Lukeneder and Adrienne Jochum
During the past years, interest in the processing and preservation of historical, scientific collections has increased significantly. Fascinating and obscure treasures are stored along with their individual stories while splendid and exciting specimens eke out an existence in boxes and cellars. The scientific curation of the Dominik Bilimek (1813-1884) Collection at BOKU University (Vienna, Austria) is one such example. Stored in the attic for many decades, later stashed in the basement, surviving two floods, a plethora of untold narratives unfolded as the specimens were unpacked. For example, the story of the young, aspiring, Slovenian collector and researcher, Heinrich Hauffen (1836-1866), with his special interests in speleology and the fauna inhabiting the subterranean realm come to light.
The only known photograph of collector and naturalist Heinrich Hauffen (1836-1866) (Digital Library of Slovenia; reference number 5S74D58Z).
At first, it was just a label type in the collection that differed from the others. It was a multidisciplinary process to assign it to Hauffen. At that time, only few scientists were concerned with the genus Carychium, including Georg von Frauenfeld (1807-1873), Heinrich Freyer (1802-1866), and Meinrad Thaurer von Gallenstein (1811-1872), all of whom were names that were closely linked to Bilimek and his collection. Fortunately, Hauffen’s handwriting could be identified by using original manuscripts from the Archive of the National Museum of Slovenia.
In our work published in Subterranean Biology, we present our results on the rediscovery of historical material of Heinrich Hauffen, which turned out to be original material, that he used to describe the cave snail taxa Carychium reticulatum and Carychium reticulatum bidentatum. Today, the eastern Alpine and the Dinaric subterranean members of the genus Carychium are assigned to their own genus, Zospeum, based on their troglobiontic characteristics such as lack of eyes, colourless bodies, genetic data, and their totally different shell morphology.
Live animal, indicated by the yellow arrow, of the genus Zospeum from Krska jama cave in Slovenia. The snail’s shell appears almost to be translucent.
This interdisciplinary work not only includes historical aspects, but also a collaboration with the Natural History Museum Vienna and the Department of Evolutionary Biology (University of Vienna) in conjunction with the taxonomic expertise from the Natural History Museum Bern (Bern, Switzerland), the Senckenberg Research Institute and Natural History Museum (Frankfurt am Main, Germany) and from the Zoologische Staatssammlung München (Münich, Germany). By using light microscopy, X-ray Micro-CT data and SEM in sync with Hauffen’s original figures and handwritten documents, the morphological analysis of C. reticulatum illustrates the degree of phenotypic variation on the shells of individuals from two different cave populations of the species Zospeum spelaeum. The species Carychium bidentatum is considered a junior synonym of Zospeum costatum.
Cave snail collection during field work in Slovenia and Spain.
The genus Zospeum constitutes a radiation of minute, glassy troglobitic snails (Ellobioidea) endemic to the Eastern Alps and the Dinaric Alps, extending as far west as Lake Garda in Italy and as far south as Montenegro. So far, 38 species of Zospeum have been described. Morphologically, the most informative diagnostic characters are apertural form and the degree of coiling and the shape of the columella (inner spindle) as well as the presence and configuration of the lamella in relation to it. In the Pre-Micro-CT era, one had to poke windows into the shells to view these signatory structures. Valuable material could become damaged, and many taxonomists shied from risky mishaps to assess the tiny shells (< 1.5 mm). This present work demonstrates the efficacy of fine-resolution imagery to assess valuable historic material.
Archive of the Institute of Applied Geology (BOKU University), where the Bilimek Collection including Hauffen’s material, is being stored and processed. Photo by Radek Polách, Muzea Novojičínska.
Hauffen died at the age of 30 as part of the Austrian volunteer corps in Mexico – with the prospect of a permanent position at the Mexican National Museum. According to current knowledge, this is the reason why the Hauffen collection was passed on to Bilimek, who returned to Europe in 1867. There are still abundant specimens, often from localities that cannot longer be sampled nowadays, from Hauffen within the Bilimek collection. In the future, this part can hopefully be separated and scientifically processed as well.
Research article:
Lukeneder P, Ottner F, Harzhauser M, Winkler V, Metscher B, Ruthensteiner B, Jochum A (2024) Lost & Found – Rediscovery of H. Hauffen’s Carychium material in the Dominik Bilimek Collection, BOKU University, including a contemporary assessment within the genus Zospeum (Gastropoda, Ellobioidea, Carychiinae). Subterranean Biology 49: 97-116. https://doi.org/10.3897/subtbiol.49.130692
The International Congress of Entomology 2024 (ICE2024), which took place on August 25-30 2024 in Kyoto, Japan, was arguably the biggest entomology event of the year. For the Pensoft team, it was an excellent chance to catch up with our authors and editors and discuss new partnerships.
At the Kyoto International Conference Center, entomologists visited lectures, symposia, and poster presentations, but they also enjoyed insect-themed haikus, origami, and artworks, and got to sample some edible insects.
— International Congress of Entomology 2024 Kyoto JP (@ice2024kyoto_jp) August 27, 2024
Meeting our authors in person was a chance for us to gather valuable feedback and make sure we are doing our best to provide entomologists with a frictionless process that makes their published research shine.
Robin Kundrata, author in ZooKeys
Deepa Pureswaran, author and editor in NeoBiota
Alain Roques, author and editor in NeoBiota
Jessica Gillung, author in ZooKeys
Ranjith AP, editor in Check List and author in ZooKeys and Journal of Hymenoptera Research
Scientific illustrator Denitsa Peneva’s beautiful works adorned Pensoft’s stand; Mostafa Ghafouri Moghaddam, subject editor at ZooKeys and Biodiversity Data Journal and author at a number of Pensoft-published journals even got to take one of her prints home after winning a raffle that Pensoft organised. He won a beautiful illustration of Bombus fragrans on Trifolium pratense.
Pensoft’s founder and CEO and one of the founding editors of the company’s flagship journal ZooKeys, Prof. Lyubomir Penev, was there representing the company and meeting with fellow entomologists.
Prof. Penev with Evgeny Zakharov of the Centre for Biodiversity Genomics
Prof. Penev with researchers Jadranka Rota, Niklas Wahlberg, Alexander Konstantinov, and Michael Schmidt
Prof. Penev with researcher Caroline S. Chaboo
They also got the chance to learn about the ARPHA Platform, a next-generation publishing solution that offers a streamlined and efficient workflow for authors, reviewers, and editors.
At ICE2024, Pensoft also presented its newest open-access jorunal, Natural History Collections and Museomics. A peer-reviewed journal for research, discussion and innovation of natural history collections, NHCM will publish under a diamond open access model, allowing free access to published content without any fees for authors or readers.
In addition to its publishing endeavors, Pensoft also presented some of the EU-funded pollinator projects that it takes part in such as Safeguard, PollinERA, and WildPosh.
ICE2024 was a chance to advance entomological science and foster collaboration within the global scientific community. For those who missed the chance to connect with Pensoft in Kyoto, the company’s journals and platforms remain accessible online, offering opportunities to read and produce groundbreaking research in insect diversity and ecology.
The indexing is one of the major outcomes from the partnerships within the Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL)
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.
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.
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.
***
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.
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.
October and November 2023 were active months for the Pensoft team, who represented the publisher’s journals and projects at conferences in Europe, North America, South America, Oceania and Asia.
Let’s take a look back at all the events of the past two months.
The Biodiversity Information Standards Conference 2023
The annual gathering is a crucial platform for sharing insights, innovations, and knowledge related to biodiversity data standards and practices. Key figures from Pensoft took part in the event, presenting new ways to improve the management, accessibility, and usability of biodiversity data.
Prof. Lyubomir Penev, founder and Chief Executive Officer of Pensoft, gave two talks that highlighted the importance of data publishing. His presentation on “The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data” underscored the significance of FAIR (Findable, Accessible, Interoperable, and Reusable) data standards. BKH is the major output from the Horizon 2020 project BiCIKL (Biodiversity Community Integrated Knowledge Library) dedicated to linked and FAIR data in biodiversity, and coordinated by Pensoft.
Prof. Lyubomir Penev, Pensoft founder and CEO.
He also introduced the Nanopublications for Biodiversity workflow and format: a promising new tool developed by Knowledge Pixels and Pensoft to communicate key scientific statements in a way that is human-readable, machine-actionable, and in line with FAIR principles. Earlier this year, Biodiversity Data Journal integrated nanopublications into its workflow to allow authors to share their findings even more efficiently.
Chief Technology Officer of Pensoft Teodor Georgiev contributed to the conference by presenting “OpenBiodiv for Users: Applications and Approaches to Explore a Biodiversity Knowledge Graph.” His session highlighted the innovative approaches being taken to explore and leverage a biodiversity knowledge graph, showcasing the importance of technology in advancing biodiversity research.
Metabarcoding and Metagenomics editor-in-chief, Florian Leese.
The theme of the conference was “Monitoring Biodiversity for Action” and there was particular emphasis on the development of best practices and new technologies for biodiversity observations and monitoring to support transformative policy and conservation action.
Metabarcoding & Metagenomics’ editor-in-chief, Florian Leese, was one of the organisers of the “Standardized eDNA-Based Biodiversity Monitoring to Inform Environmental Stewardship Programs” session. Furthermore, the journal was represented at Pensoft’s exhibition booth, where conference participants were able to discuss metabarcoding and metagenomics research.
#geobonconf2023 was great as it linked different actors performing #biodiversity monitoring. Today we discussed #eDNA standardisation. We need formal standards, QA/QC, guidance, 🌐harmonisation to facilitate uptake. Cool to see our @DNAquaNet practical guide in this context. pic.twitter.com/eTOtr3yug8
Following the conference, Metabarcoding & Metagenomics announced a new special issue titled “Towards Standardized Molecular Biodiversity Monitoring.” The special issue is accepting submissions until 15th March 2024.
Asian Mycological Congress2023
The Asian Mycological Congress welcomed researchers from around the world to Busan, Republic of Korea, for an exploration of all things fungi from 10-13 October.
MycoKeys Best Talk award (winner not pictured).
Titled “Fungal World and Its Bioexploitation – in all areas of basic and applied mycology,” the conference covered a range of topics related to all theoretical and practical aspects of mycology. There was a particular emphasis on the development of mycology through various activities associated with mycological education, training, research, and service in countries and regions within Asia.
As one of the sponsors of the congress, Pensoft proudly presented a Best Talk award to Dr Sinang Hongsanan of Chiang Mai University, Thailand. The award entitles the winner to a free publication in Pensoft’s flagship mycology journal, MycoKeys.
Joint ESENIAS and DIAS Scientific Conference 2023
The ESENIAS and DIAS conference took place from 11-14 October and focused on “globalisation and invasive alien species in the Black Sea and Mediterranean regions.” Pensoft shared information on their NeoBiota journal and the important REST-COAST and B-Cubed projects.
Polina Nikova receiving the NeoBiota Best Talk Award.
Polina Nikova of the Bulgarian Academy of Sciences received the NeoBiota Best Talk Award for her presentation titled “First documented records in the wild of American mink (Neogale vision von Schreber, 1776) in Bulgaria.” The award entitles her to a free publication in the NeoBiota journal.
XII European Congress of Entomology
Pensoft took part in the XII European Congress of Entomology (ECE 2023) in Heraklion, Crete, from 16-20 October. The event provided a forum for entomologists from all over the world, bringing together over 900 scientists from 60 countries.
Carla Stoyanova, Teodor Metodiev and Boriana Ovcharova representing Pensoft.
The ECE 2023, organised by the Hellenic Entomological Society, addressed the pressing challenges facing entomology, including climate change, vector-borne diseases, biodiversity loss, and the need to sustainably feed a growing world population. The program featured symposia, lectures, poster sessions, and other types of activities aimed at fostering innovation in entomology. For Pensoft, they were a great opportunity to interact with scientists and share their commitment to advancing entomological research and addressing the critical challenges in the field.
🐝Today at #ECE2023, Prof Denis Michez & Sara Reverté are running a workshop on bee identification!
Throughout the event, conference participants could find Pensoft’s team at thir booth, and learn more about the scholarly publisher’s open-access journals in entomology. In addition, the Pensoft team presented the latest outcomes from the Horizon 2020 projects B-GOOD, Safeguard, and PoshBee, where the publisher takes care of science communication and dissemination as a partner.
Group photo of XIV International Congress of Orthopterology 2023 participants.
Hosted for the first time in Mexico, it attracted experts and enthusiasts from around the world. The congress featured plenary speakers who presented cutting-edge research and insights on various aspects of grasshoppers, crickets, and related insects.
Pensoft’s Journal of Orthoptera Research was represented by Tony Robillard, the editor-in-chief, who presented the latest developments of the journal to attendees.
Symposia, workshops, and meetings facilitated discussions on topics like climate change impacts, conservation, and management of Orthoptera. The event also included introductions to new digital and geospatial tools for Orthoptera research.
The 16th International Conference on Ecology and Management of Alien Plant Invasions
4th International ESP Latin America and Caribbean Conference
The 4th International ESP Latin America and Caribbean Conference (ESP LAC 2023) was held in La Serena, Chile, from 6-10 November. Focused on “Sharing knowledge about ecosystem services and natural capital to build a sustainable future,” the event attracted experts in ecosystem services, particularly from Latin America and the Caribbean.
🤩 So excited to be part of the 4th International ESP Latin America and Caribbean Conference, which opens later today! In a great tradition with the ESP conferences, we are offering three full APC waivers for the three best posters.@ESPartnershiphttps://t.co/O97nwEGnMj
Organised by the Ecosystem Services Partnership, this bi-annual conference was open to both ESP members and non-members, featuring a hybrid format in English and Spanish. Attendees enjoyed an excursion to La Serena’s historical center, adding a cultural dimension to the event.
The conference included diverse sessions and a special recognition by Pensoft’s One Ecosystem journal, which awarded full waivers for publication to the authors of the three best posters.
Magaly Aldave receiving the Best Poster Award.
Magaly Aldave of the Transdisciplinary Center for FES-Systemic Studies claimed first prize with “The voice of children in the conservation of the urban wetland and Ramsar Site Pantanos de Villa in Metropolitan Lima, Peru.” Ana Catalina Copier Guerrero and Gabriela Mallea-Rebolledo, both of the University of Chile, were awarded second and third prize respectively.
The event featured in-person and online participation, catering to a wide audience of researchers, academics, and students. It included workshops, presentations, and discussions, with a focus on enhancing understanding in biosystematics.
Pensoft awarded three student prizes at the event. Putter Tiatragu, Australian National University, received the Best Student Talk award and a free publication in any Pensoft journal for “A big burst of blindsnakes: Phylogenomics and historical biogeography of Australia’s most species-rich snake genus.”
Helen Armstrong, Murdoch University, received the Best Student Lightning Talk for “An enigmatic snapper parasite (Trematoda: Cryptogonimidae) found in an unexpected host.” Patricia Chan, University of Wisconsin-Madison, was the Best Student Lightning Talk runner-up for “Drivers of Diversity of Darwinia’s Common Scents and Inflorescences with Style: Phylogenomics, Pollination Biology, and Floral Chemical Ecology of Western Australian Darwinia (Myrtaceae).”
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As we approach the end of 2023, Pensoft looks back on its most prolific and meaningful year of conferences and events. Thank you to everyone who contributed to or engaged with Pensoft’s open-access journals, and here’s to another year of attending events, rewarding important research, and connecting with the scientific community.
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.
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.
Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.
Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability.
By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data.
With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable mannerin line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.
The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards.
Now, what’s new?
As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:
Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).
Nanopublications for biodiversity data?
At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proofthe most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments.
On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.
Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:
So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences.
Nanopublication template customised for biodiversity research publications available from Nanodash.
As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks.
The novel domain-specific publication format was launched as part of thecollaboration betweenKnowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisherPensoft.
Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.
These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.
In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs.
“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”
By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragmentsof scientific information is interconnected and traceable back to its author(s) and scientific evidence.
A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels.
By building on shared knowledge representation models, these data become Interoperable (as in the Iin FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts.
Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.
A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way.
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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal.
Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!
On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.
Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.
Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.
Australia’s rich and diverse fauna never fails to surprise us, as a new spider species has been documented from the continent.
The novel species, a blind daddy long-legs, was found in boreholes in the arid Pilbara of Western Australia. It is the first cave-adapted daddy long-legs spider reported from the continent, with other blind species of its genus so far only found in Thailand, Laos, and Vietnam.
Belisana coblynau, male.
“It represents a subfamily that was previously thought to be restricted to the tropical north and east of the continent,” says Bernhard Huber, one of the authors of a recent study published in the journal Subterranean Biology.
“The new species suggests that these spiders were widely distributed in Australia before the continent’s aridification in the last tens of millions of years,” he adds.
Together with it, another extraordinary daddy long-legs species was described as new-to-science from Réunion island. It was collected in the Grotte de La Tortue, a 300,000-year-old lava tube. Its closest known relatives are in eastern Africa, which begs the question how the species reached the island.
Grotte de La Tortue. Photos by Credit T. Percheron
The researchers believe its ground-dwelling ancestor arrived to Réunion “relatively recently and by highly accidental means (such as rafts or storms)” but adapted quickly to subterranean life.
“If our generic assignment is correct, then the ancestor of Buitinga ifrit must have reached Réunion from East Africa within the last few million years,” they write in their paper.
Buitinga ifrit, male.
Curiously, both spiders were named after mythical underground dwellers: Belisana coblynau,after “the mythical gnome-like creatures that are said to haunt mines and quarries,” and Buitinga ifrit, after “a demon in Islamic mythology that is often associated with the underworld.”
Original source:
Huber BA, Meng G, Clark HL, Cazanove G (2023) First blind daddy long-legs spiders from Australia and Réunion (Araneae, Pholcidae). Subterranean Biology 46: 1-19. https://doi.org/10.3897/subtbiol.46.105798
All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research.
As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service.
According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.
While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals.
This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.
“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”
said Robert Kiley, Head of Strategy at cOAlition S.
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About cOAlition S:
On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.
About Plan S:
Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.
