What we thought we knew about carnivorous plants was swiftly called into question after scientists discovered a new species in the Indonesian province of North Kalimantan, on the island of Borneo. Nepenthes pudica is what scientists call a pitcher plant – it has modified leaves known as pitfall traps or pitchers, where it captures its prey. In a strategy so far unknown from any other species of carnivorous plant with pitfall traps, this one operates underground, catching its prey in the soil.
“We found a pitcher plant which differs markedly from all the other known species,” says Martin Dančák of Palacký University in Olomouc, Czech Republic, lead author of the study, published in the journal PhytoKeys, where his team described the new species.
“In fact, this species places its up-to-11-cm-long pitchers underground, where they are formed in cavities or directly in the soil and trap animals living underground, usually ants, mites and beetles”, he adds.
Only three other groups of carnivorous plants are known to trap underground prey, but they all use very different trapping mechanisms and, unlike Nepenthes pudica, can catch only minuscule organisms.
The plant forms specialised underground shoots with entirely white, chlorophyll-free leaves. In addition to lacking their normal green pigmentation, the leaves supporting the pitchers are reduced to a fraction of their normal size. The pitchers, however, retain their size and often also their reddish colour.
“Interestingly, we found numerous organisms living inside the pitchers, including mosquito larvae, nematodes and a species of worm which was also described as a new species”, explains Václav Čermák of the Mendel University in Brno, Czech Republic, who was also part of the research team.
The newly discovered species grows on relatively dry ridge tops at an elevation of 1100–1300 m. According to its discoverers, this might be why it evolved to move its traps underground. “We hypothesise that underground cavities have more stable environmental conditions, including humidity, and there is presumably also more potential prey during dry periods,” adds Michal Golos of the University of Bristol, United Kingdom, who also worked on this curious plant.
A series of lucky events back in 2012 led to the discovery of the species. Ľuboš Majeský of Palacký University Olomouc, part of the research team, recounts the key moment: “During a several-day trip with our Indonesian colleagues to a previously unexplored mountain, randomly chosen from a number of candidates, we noted plants which were undoubtedly Nepenthes but produced no pitchers. After a careful search, we found a couple of aerial pitchers, a few juvenile terrestrial ones, and one deformed pitcher protruding from the soil.”
“At first, we thought it was an accidentally buried pitcher and that local environmental conditions had caused the lack of other pitchers. Still, as we continued to find other pitcherless plants along the ascent to the summit, we wondered if a species of pitcher plant might have evolved towards loss of carnivory, as seen in some other carnivorous plants. But then, when taking photos, I tore a moss cushion from a tree base revealing a bunch of richly maroon-coloured pitchers growing from a short shoot with reduced leaves entirely lacking chlorophyll.”
The group then checked the other encountered plants and found that all of them had underground shoots with pitchers, confirming that this species specifically targets the underground environment.
The scientific name Nepenthes pudica points to the plant’s curious behaviour: it is derived from the Latin adjective pudicus, which means bashful and reflects the fact that its lower pitchers remain hidden from sight.
Nepenthes pudica is endemic to Borneo. “This discovery is important for nature conservation in Indonesian Borneo, as it emphasises its significance as a world biodiversity hotspot. We hope that the discovery of this unique carnivorous plant might help protect Bornean rainforests, especially prevent or at least slow the conversion of pristine forests into oil palm plantations”, concludes Wewin Tjiasmanto of Yayasan Konservasi Biota Lahan Basah, who helped discover the new species.
Dančák M, Majeský Ľ, Čermák V, Golos MR, Płachno BJ, Tjiasmanto W (2022) First record of functional underground traps in a pitcher plant: Nepenthes pudica (Nepenthaceae), a new species from North Kalimantan, Borneo. PhytoKeys 201: 77-97. https://doi.org/10.3897/phytokeys.201.82872
Ask any scientist — for every “Eureka!” moment, there’s a lot of less-than-glamorous work behind the scenes. Making discoveries about everything from a new species of dinosaur to insights about climate change entails some slogging through seemingly endless data and measurements that can be mind-numbing in large doses.
Community science shares the burden with volunteers who help out, for even just a few minutes, on collecting data and putting it into a format that scientists can use. But the question remains how useful these data actually are for scientists.
A new study, authored by a combination of high school students, undergrads and grad students, and professional scientists showed that when museum-goers did a community science activity in an exhibit, the data they produced were largely accurate, supporting the argument that community science is a viable way to tackle big research projects.
“We were able to combine a small piece of the Field Museum’s vast collections, their scientific knowledge and exhibit creation expertise, the observational skills of biology interns at Northeastern Illinois University (USA), led by our collaborator Tom Campbell, and our Roosevelt University student’s data science expertise. The creation of this set of high-quality data was a true community effort!”
The study focuses on an activity in an exhibition at the Field Museum, in which visitors could partake in a community science project. In the community science activity, museumgoers used a large digital touchscreen to measure the microscopic leaves photographs of plants called liverworts.
These tiny plants, the size of an eyelash, are sensitive to climate change, and they can act like a canary in a coal mine to let scientists know about how climate change is affecting a region. It’s helpful for scientists to know what kinds of liverworts are present in an area, but since the plants are so tiny, it’s hard to tell them apart. The sizes of their leaves (or rather, lobes — these are some of the most ancient land plants on Earth, and they evolved before true leaves had formed) can hint at their species. But it would take ages for any one scientist to measure all the leaves of the specimens in the Field’s collection. Enter the community scientists.
“Drawing a fine line to measure the lobe of a liverwort for a few hours can be mentally strenuous, so it’s great to have community scientists take a few minutes out of their day using fresh eyes to help measure a plant leaf. A few community scientists who’ve helped with classifying acknowledged how exciting it is knowing they are playing a helping hand in scientific discovery,”
says Heaven Wade, a research assistant at the Field Museum who began working on the MicroPlants project as an undergraduate intern.
Community scientists using the digital platform measured thousands of microscopic liverwort leaves over the course of two years.
“At the beginning, we needed to find a way to sort the high quality measurements out from the rest. We didn’t know if there would be kids drawing pictures on the touchscreen instead of measuring leaves or if they’d be able to follow the tutorial as well as the adults did. We also needed to be able to automate a method to determine the accuracy of these higher quality measurements,”
To answer these questions, Pivarski worked with her students at Roosevelt University to analyze the data. They compared measurements taken by the community scientists with measurements done by experts on a couple “test” lobes; based on that proof of concept, they went on to analyze the thousands of other leaf measurements. The results were surprising.
“We were amazed at how wonderfully children did at this task; it was counter to our initial expectations. The majority of measurements were high quality. This allowed my students to create an automated process that produced an accurate set of MicroPlant measurements from the larger dataset,”
The researchers say that the study supports the argument that community science is valuable not just as a teaching tool to get people interested in science, but as a valid means of data collection.
Pivarski M, von Konrat M, Campbell T, Qazi-Lampert AT, Trouille L, Wade H, Davis A, Aburahmeh S, Aguilar J, Alb C, Alferes K, Barker E, Bitikofer K, Boulware KJ, Bruton C, Cao S, Corona Jr. A, Christian C, Demiri K, Evans D, Evans NM, Flavin C, Gillis J, Gogol V, Heublein E, Huang E, Hutchinson J, Jackson C, Jackson OR, Johnson L, Kirihara M, Kivarkis H, Kowalczyk A, Labontu A, Levi B, Lyu I, Martin-Eberhardt S, Mata G, Martinec JL, McDonald B, Mira M, Nguyen M, Nguyen P, Nolimal S, Reese V, Ritchie W, Rodriguez J, Rodriguez Y, Shuler J, Silvestre J, Simpson G, Somarriba G, Ssozi R, Suwa T, Syring C, Thirthamattur N, Thompson K, Vaughn C, Viramontes MR, Wong CS, Wszolek L (2022) People-Powered Research and Experiential Learning: Unravelling Hidden Biodiversity. Research Ideas and Outcomes 8: e83853. https://doi.org/10.3897/rio.8.e83853
You might think that Europe is so well studied that no large animals remain undiscovered. Yet today, a new species of giant keelback slug from Montenegro was announced in the open-access Biodiversity Data Journal. The animal, as big as a medium-sized carrot, was discovered on a citizen-science expedition and jointly described by its participants.
The international team of citizen scientists from Italy, the Netherlands, Serbia, South Africa, and the United States found the slug in July 2019 while exploring the spectacular Tara Canyon, Europe’s deepest gorge, on inflatable rafts. The brownish-grey animals, with a sharp ridge along the back, and 20 cm in length when fully stretched, were hiding under rocky overhangs in the narrowest part of the ravine.
At first, the newly discovered slugs seemed superficially indistinguishable from the ash-black keelback slug (Limax cinereoniger), which also lives in the Tara Canyon. The team had to use a portable DNA lab to work out that there is a 10% difference between the two slugs in the so-called DNA barcode. Moreover, when they dissected a few of them, they found differences in the reproductive organs as well. This was enough to decide that a new species had been discovered, and they named it Limax pseudocinereoniger to indicate its similarity to L. cinereoniger.
The field trip was run by Taxon Expeditions, which organises real scientific expeditions for the general public, with the aim to make scientific discoveries. Rick de Vries, a web editor and illustrator from Amsterdam who found the first specimen of L. pseudocinereoniger, says: “It’s an incredible thrill to hold an animal in your hands and to know that it is still unknown to science”.
Zoologist Iva Njunjić, one of the authors of the paper, thinks that more unknown species are likely to be found in Tara Canyon and the Durmitor National Park, of which it is part. “Using a combination of DNA analysis and anatomy will probably reveal more species that are identical on the outside but actually belong to different species,” she says.
In 2023, Taxon Expeditions plans to take a new team of citizen scientists to Montenegro with a mission to discover new species and document the hidden biodiversity.
Taxon Expeditions was founded by Iva Njunjić and Menno Schilthuizen of Naturalis Biodiversity Center and specialises in ‘taxonomy tourism’ trips in Brunei, Italy, Montenegro, Panama, and the Netherlands.
Schilthuizen M, Thompson CG, de Vries R, van Peursen ADP, Paterno M, Maestri S, Marcolongo L, Esposti CD, Delledonne M, Njunjić I (2022) A new giant keelback slug of the genus Limax from the Balkans, described by citizen scientists. Biodiversity Data Journal 10: e69685. https://doi.org/10.3897/BDJ.10.e69685
So far, science has described more than 2 million species, and millions more await discovery. While species have value in themselves, many also deliver important ecosystem services to humanity, such as insects that pollinate our crops.
Meanwhile, as we lack a standardized system to quantify the value of different species, it is too easy to jump to the conclusion that they are practically worthless. As a result, humanity has been quick to justify actions that diminish populations and even imperil biodiversity at large.
In a study, published in the scholarly open-science journal Research Ideas and Outcomes, a team of Estonian and Swedish scientists propose to formalize the value of all species through a conceptual species ‘stock market’ (SSM). Much like the regular stock market, the SSM is to act as a unified basis for instantaneous valuation of all items in its holdings.
However, other aspects of the SSM would be starkly different from the regular stock market. Ownership, transactions, and trading will take new forms. Indeed, species have no owners, and ‘trade’ would not be about transfer of ownership rights among shareholders. Instead, the concept of ‘selling’ would comprise processes that erase species from some specific area – such as war, deforestation, or pollution.
Conversely, taking some action that benefits biodiversity – as estimated through individuals of species – would be akin to buying on the species stock market. Buying, too, has a price tag on it, but this price should probably be thought of in goodwill terms. Here, ‘money’ represents an investment towards increased biodiversity.
Interestingly, the SSM revolves around the notion of digital species. These are representations of described and undescribed species concluded to exist based on DNA sequences and elaborated by including all we know about their habitat, ecology, distribution, interactions with other species, and functional traits.
For the SSM to function as described, those DNA sequences and metadata need to be sourced from global scientific and societal resources, including natural history collections, sequence databases, and life science data portals. Digital species might be managed further by incorporating data records of non-sequenced individuals, notably observations, older material in collections, and data from publications.
The study proposes that the SSM is orchestrated by the international associations of taxonomists and economists.
“Non-trivial complications are foreseen when implementing the SSM in practice, but we argue that the most realistic and tangible way out of the looming biodiversity crisis is to put a price tag on species and thereby a cost to actions that compromise them,”
The BiCIKL project is dedicated to building new communities of key research infrastructures, researchers, citizen scientists and other stakeholders by using linked and FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing and identification of taxa, to final publication in advanced, human- and machine-readable, reusable scholarly articles.
Supported by BiCIKL, the upcoming collection at BDJ will provide an exciting opportunity for biodiversity researchers to enjoy free and technologically advanced publication for up to 100 scholarly articles.
The collection will welcome research articles, data papers, software descriptions, and methodological/theoretical papers that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
The journal is still looking for guest editors to join the core team. If you are interested, please let us know at firstname.lastname@example.org.
In this collection, the authors will need to ensure that their narratives comply with the community-agreed standards for terms, ontologies and vocabularies. Additionally, they will be required to use explicit persistent identifiers, where such are available.
Here are several examples of research questions concerning semantically enriched biodiversity data:
How linking taxa or OTUs to external data in my study will contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
How mine and other researchers’ data and narratives (e.g. specimen records, sequences, traits, biotic interactions etc.) can be re-used to support more extensive and data-rich studies?
How to streamline taxon descriptions and inventories, including such based on genomic and barcoding data?
How general conclusions, assertions and citations in my article can be expressed in a formal, machine-actionable language?
Other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR data.
Taxonomic papers (e.g. descriptions of new species) must contain persistent identifiers for the holotype, paratypes and the majority of the specimens used in the study.
New species descriptions using data associated with a particular Barcode Identification Number (BIN) imported directly from BOLD via the ARPHA Writing Tool are encouraged.
Individual specimen records imported directly from BOLD, GBIF or iDigBio into the manuscript are strongly encouraged.
Hyperlinked in-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome.
Other terms of value hyperlinked to external resources are encouraged.
Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s guidelines.
Theoretical or methodological papers on linking of FAIR biodiversity data are eligible for the BiCIKL collection if they provide examples and use cases.
Data papers or software descriptions are eligible if they use data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.
You can find full information about the eligibility criteria in the Open Call published on the BiCIKL’s website, or can contact us at email@example.com.
The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.
The BiCIKL project invites submissions of Expression of Interest (EoI) to the First BiCIKL Open Call for projects. The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.
By opening this call, BiCIKL aims to better understand how it could support scientific questions that arise from across the biodiversity world in the future, while addressing specific scientific or technical biodiversity data challenges presented by the applicants.
The BiCIKL project – a Horizon 2020-funded project involving 14 European institutions, representing major global players in biodiversity research and natural history, and coordinated by Pensoft – establishes a European starting community of key research infrastructures, researchers, citizen scientists and other biodiversity and life sciences stakeholders based on open science practices through access to data, tools and services.
Somatic growth rate is a central life-history parameter, especially in species like fishes or invertebrates which grow throughout their lives. It is needed in conservation and fisheries management but it can sometimes be tricky to estimate.
Dr. Froese presents two new data-limited methods to estimate somatic growth from maximum length combined with either length or age at maturation or with maximum age. They are applicable to a wide range of species, sizes, and habitats. Using these new methods, growth parameter estimates were produced for the first time for 110 fish species.
“The growth estimates derived with the new methods presented in this study appear suitable for consideration and preliminary guidance in applications for conservation or management,” Dr. Froese points out in his study.
He goes on to suggest that journals accept growth estimates performed with the new methods as new knowledge, if they are the first for a given species.
In order to facilitate the conservation and management of natural resources, FishBase will continue to compile growth parameters, including results obtained with these new methods.
Amongst tetrapods, amphibians entail the highest number of threatened and data deficient species, which has put them in the limelight of research in animal ecology and conservation. Endemic species have evolved and adapted to a particular set of environmental conditions. Hence, these are more vulnerable to environmental changes and are susceptible to population declines because of their restricted distribution ranges.
The Murree Hills Frog and Hazara Torrent Frog are endemic to Pakistan and South Asian countries. They are associated with the torrential streams and nearby clear water pools situated at high elevation. These frogs are susceptible to threats like habitat degradation, urbanization, and climate change. A recent study published in the-open access journal Biodiversity Data Journal reports that these endemic frogs do not show much movement within and outside their habitat.
“We have, for the first time, used radio-transmitters (VHF) on frogs endemic to Himalayan region to understand their ecology,” explains Dr. Muhammad Rais, Assistant Professor at the Herpetology Lab in the Arid Agriculture University, Rawalpindi, and lead author of the study. “Surprisingly, the Murree Hills Frog and Hazara Torrent Frog depend heavily for their survival on particular stream(s).”
“We suggest carrying out additional long term studies by incorporating multiple adjacent stream systems to better understand dispersal and colonization in these frogs,” he says in conclusion.
Akram A, Rais M, Saeed M, Ahmed W, Gill S, Haider J (2022) Movement Paradigm for Hazara Torrent Frog Allopaa hazarensis and Murree Hills Frog Nanorana vicina (Anura: Dicroglossidae). Biodiversity Data Journal 10: e84365. https://doi.org/10.3897/BDJ.10.e84365
Deep in the forests of Odisha and Andhra Pradesh in India lives a colourful gecko species that only now revealed its true identity. Meet Eublepharis pictus, also known as the Painted Leopard Gecko.
In 2017, researchers Zeeshan A. Mirza of theNational Centre for Biological Sciences in Bangalore and C. Gnaneswar of theMadras Crocodile Bank Trust in Chennai found a gecko in a water tank near a temple in Vishakhapatnam, Andhra Pradesh, during a field survey. Back then, they identified it as belonging to the East Indian Leopard Gecko species (Eublepharis hardwickii).
“The species appears to be common in the hill forests, but its distinctness was only confirmed by other researchers,” Zeeshan Mirza explains.
In a phylogenetic study, where they looked for the evolutionary history and relationships within and between the leopard gecko species in the genus Eublepharis, the researchers found that what had until then been considered a southern population of East Indian Leopard Geckomight be distinct enough to represent a new species.
Once they had molecular data they could work with, the team made morphological comparisons between the species, looking at specimens across natural history museums.
“These lizards have conserved morphologies and most species are quite similar in general appearance,” Zeeshan Mirza elaborates. “With a few characters based on the number of specimens examined, we described the species and named it the Painted Leopard Gecko – in Latin, Eublepharis pictus, for its colouration.” Theypublished their discovery in the open-access scientific journalEvolutionary Systematics.
With this new addition, the gecko genus Eublepharis now contains 7 species. Two of them – E. pictus and E. satpuraensis – were described by Zeeshan Mirza.
The Painted Leopard Gecko measures 11.7 cm in length, which is somewhat large for a leopard gecko. The Brahmani River, which runs through the Eastern Ghats, separates it geographically from the East Indian Leopard Gecko, with which it shares a lot of similar traits.
The new species lives in dry evergreen forests mixed with scrub and meadows. It is strictly nocturnal, actively foraging along trails in the forest after dusk. While looking for food, it has been observed licking surfaces as it moves, which suggests it might use its tongue as a sensory organ.
Even though the Painted Leopard Gecko seems to be widespread across the state of Odisha and northern Andhra Pradesh, the researchers worry about its conservation. “The species is collected for the pet trade and even now may be smuggled illegally,” they write in their paper, which is why they refrain from giving out the exact locations where it may be found.
The authors believe the species would stand more of a chance against humans if more people knew it was actually harmless. To protect it, they suggest listing it as Near Threatened based on IUCN conservation prioritisation criteria, until more is known about the size of its populations.
Further research may also encourage better protection of biodiversity in the area. “The Eastern Ghats are severely under-surveyed, and dedicated efforts will help recognize it as a biodiversity hotspot,” the authors conclude.
Mirza ZA, Gnaneswar C (2022) Description of a new species of leopard geckos, Eublepharis Gray, 1827 from Eastern Ghats, India with notes on Eublepharis hardwickii Gray, 1827. Evolutionary Systematics 6(1): 77-88.https://doi.org/10.3897/evolsyst.6.83290
It was in late 1992 when biologist and ecologist Prof Dr Lyubomir Penev in a collaboration with his friend Prof. Sergei Golovatch established Pensoft: a scholarly publisher with the ambition to contribute to novel and even revolutionary methods in academic publishing by applying its own approach to how science is published, shared and used. Inspired by the world’s best practices in the field, Pensoft would never cease to view the issues and gaps in scholarly publishing in line with its slogan: “by scientists, for scientists”.
As we celebrate the 30th anniversary of Pensoft, we are asking ourselves: What’s a tree without its roots?
That’s why we’ve put up an attractive timeline of Pensoft’s milestones on our website, and complemented it with some key figures, in an attempt to translate those years into numbers. Yet, one can say only that much in figures. Below, we’ll give a bit more context and background about Pensoft’s key milestones.
1994: Pensoft publishes its first book & book series
In time for New Year’s Day in 1994, we published the first book bearing the name of Pensoft. The catalogue of the sheet weaver spiders (Lyniphiidae) of Northern Asia did not only set the beginning of the publishing activities of Pensoft, but also started the extensive Pensoft Series Faunistica, which continues to this day, and currently counts over 120 titles.
2003: Pensoft joins its first EU-funded research project
By 2003, we were well-decided to expand our activities toward participation in collaborative, multinational projects, thereby building on our mission to shed light and communicate the latest scientific work done.
By participating in the FP6-funded project ALARM (abbreviation for Assessing LArge-scale environmental Risks with tested Methods), coordinated by Dr. Joseph Settele from the Helmholtz Centre for Environmental Research (Germany), we would start contributing to the making of science itself in close collaboration with another 67 institutions from across Europe. Our role at ALARM during the five years of the duration of the project was to disseminate and communicate the project outcome. At the end of the project, we also produced the highly appreciated within the community Atlas of Biodiversity Risk.
As for today, 19 years later, Pensoft has taken part in 40 research projects as a provider of various services ranging from data & knowledge management and next-generation open access publishing; to communication, dissemination and (web)design; to stakeholder engagement; consultations; and event and project management.
Our project activities culminated last year, when we became the coordinator of a large and exciting BiCIKL project, dedicated to access to and linking of biodiversity data along the entire data and research life cycle.
2008: Pensoft launches its first scholarly journal to revolutionise & accelerate biodiversity research
Openly accessible and digital-first since the very start, the ZooKeys journal was born on a sunny morning in California during the Entomological Society of America meeting in 2007, when Prof Lyubomir Penev and his renowned colleague Dr Terry Erwin from the Smithsonian Institution agreed over breakfast that zoologists from around the world could indeed use a new-age taxonomic journal. What the community at the time was missing was a scholarly outlet that would not only present a smooth fast track for their research papers, while abiding by the highest and most novel standards in the field, but do so freely and openly to any reader at any time and in any place. Fast forward to 2021, ZooKeys remains the most prolific open-access journal in zoology.
With over 1,100 volumes published to date, ZooKeys is one of our most renowned journals with its own curious and intriguing history. You can find more about it in the celebratory blog post we published on the occasion of the journal’s 1,000th volume in late 2020.
At the time of writing, Pensoft has 21 journals under its own belt, co-publishes another 16, and provides its self-developed journal management platform ARPHA to another 35 scholarly outlets.
2010a: Pensoft launches its first journal publishing platform
By 2010, we realised that the main hurdle holding our progress as a next-age publisher of scientific knowledge was posed by the technology – or lack thereof – underlying the publishing process. We figured that – in our position of users – we were best equipped to figure what exactly this backbone structure should be made of.
This is when we released the publishing platform TRIADA, which was able to support both the editorial and the publication processes at our journals. This was also the point in time when we added “technology provider” to the Pensoft’s byline. Surely, we had so many ideas in our mind and TRIADA was only the beginning!
2010b: In the 50th issue of ZooKeys, Pensoft publishes the first semantically enhanced biodiversity research papers
Later the same year, TRIADA let us write some history. The 50th volume of ZooKeys wasn’t only special because of its number. It contained the first scholarly papers in the study of biodiversity featuring semantic enrichments.
The novelty that keeps a taxon only a click away from a list of related data, including its occurrences, genomics data, treatments, literature etc. is a feature that remains a favourite to our journals’ users to this very day. Unique to date, this workflow is one of the many outcomes of our fantastic long-time collaboration and friendship with Plazi.
2011: Journal of Hymenoptera Research becomes the first society journal to move to Pensoft
Three years after the launch of the very first Pensoft journal, we received a request from the International Society of Hymenopterists who wanted for their own journal: the Journal of Hymenoptera Research to follow the example of ZooKeys and provide to their authors, editors and readers a similar set of services and features designed to streamline biodiversity knowledge in a modern, user-friendly and highly efficient manner.
Ever since, the journal has been co-published by the Society and Pensoft, and enjoyed growing popularity and appeal amongst hymenopterists from around the world.
2013: Pensoft replaces TRIADA with its own in-house built innovative ARPHA Platform
As we said, TRIADA was merely the crude foundation of what was to become the ARPHA publishing platform: a publishing solution providing a lot more than an end-to-end entirely online environment to support the whole publishing process on both journal and article level.
On top of that, ARPHA’s publishing package includes a variety of automated and manually provided services, web service integrations and highly customisable features. With all of those, we aimed at one thing only: create a comprehensive scholarly publishing solution to our own dearest journals and all their users.
2013b: Pensoft develops an XML-based writing tool
Having just unveiled ARPHA Platform, we were quite confident that we have developed a pretty all-in publishing solution. Our journals would be launched, set up, hosted and upgraded safely under our watchful eye, while authors, editors and reviewers would need to send not a single email or a file outside of our collaborative environment from the moment they submit a manuscript to the moment they see it published, indexed and archived at all relevant databases.
Yet, we could still spot a gap left to bridge. The Pensoft Writing Tool (or what is now known as the ARPHA Writing Tool or AWT) provides a space where researchers can do the authoring itself prior to submitting a manuscript straight to the journal. It all happens within the tool, with co-authors, external collaborators, reviewers and editors all able to contribute to the same manuscript file. Due to the XML technology underlying AWT, various data(sets) and references can be easily imported in a few clicks, while a list of templates and content management features lets researchers spend their time and efforts on their scientific work rather than format requirements.
2015: Pensoft launches the open-science RIO Journal
Six years ago, amid heated discussions over the pros and cons of releasing scientific knowledge freely to all, we felt it’s time to push the boundaries even further.
No wonder that, at the time, a scholarly journal with the aim to bring to light ‘alternative’ research outputs from along the whole research process, such as grant proposals, project and workshop reports, data management plans and research ideas amongst many others, was seen as quite brave and revolutionary. Long story short, a year after its launch, RIO earned the honorary recognition from the Scholarly Publishing and Academic Resources Coalition (SPARC) to be named an Open Science Innovator.
Learn about the key milestones and achievements at RIO Journal to date – in addition to its future goals – in the special blog post and the editorial published on the occasion of the journal’s fifth anniversary.
2016: Pensoft provides ARPHA Platform as a white-label journal publishing solution for the first time
Led by our intrinsic understanding for scholars and smaller publishers, we saw the need of many journals and their owners to simultaneously secure a user-friendly and sustainable publishing solution for their scientific outlets. This is why we decided to also offer our ARPHA Platform as a standalone package of technology, services and features, dissociated with Pensoft as a publisher. This option is particularly useful for university presses, learned societies and institutions who would rather stick to exclusivity when it comes to their journal’s branding and imprint.
2017: Pensoft launches its conference-dedicated platforms for abstracts and proceedings
Another step forward to encompassing the whole spectrum of research outputs was to take care after conference materials: proceedings and abstracts. Once again, our thinking was that all scientific work and efforts need to be made openly available, accessible, reusable and creditable.
Both ARPHA Conference Abstracts and ARPHA Proceedings allow for organisers to conveniently bring the publications together in a conference-branded collection, thereby providing a one-stop permanent access point to all content submitted and presented at a particular event, alongside associated data, images, videos and multimedia, video recordings of conference talks or graphic files of poster presentations.
Publications at both platforms benefit from all key advantages available to conventional research papers at a Pensoft journal, such as registration at Crossref and individual DOI; publication in PDF, semantically enhanced HTML and data-minable XML formats; indexing and archiving at multiple major databases; science communications services.
2019: Pensoft develops the OpenBiodiv Knowledge Graph
As firm believers in the power and future of linked and FAIR data, at Pensoft we realise there is still a great gap in the way biodiversity data is collated, stored, accessed and made available to researchers and key stakeholders for further reuse.
In fact, this is an area within biodiversity research that is in dire need of a revolutionary mechanism to provide a readily available and convenient hub that allows a researcher to access all related data via multi-directional links interconnecting various and standardised databases, in accordance with the Web 2.0 principles.
As the first step in that direction, in 2019, we launched the OpenBiodiv Knowledge Graph, which began to collate various types of biodiversity data as extracted from semantically enhanced articles published by Pensoft and taxonomic treatments harvested by Plazi.
Since then, the OpenBiodiv Knowledge Graph has evolved into the Open Biodiversity Knowledgement Management System (OBKMS), which also comprises a Linked Open Dataset, an ontology and а website. Our work on the OBKMS continues to this day, fueled by just as much enthusiasm as in those early days in 2019.
2020: Pensoft launches ARPHA Preprints
By 2020, a number of factors and issues that had long persisted within scholarly publishing and academia had already triggered the emergence of multiple preprint servers. Yet, the onset of the unprecedented for our age COVID-19 pandemic, seemed like the final straw that made everyone realise we needed to start uncovering early scientific work, and we needed to do that fast.
At the time, we had already been considering applying the Pensoft approach to preprints. So, we came up with a solution that could seamlessly blend into our existing infrastructure.
Offered as an opt-in service to journals published on the ARPHA Platform, ARPHA Preprints allows for authors to check a box and post their manuscripts as a preprint as they are filling in the submission form at a participating journal.
Learn more about ARPHA Preprints on the ARPHA blog.
2021a: RIO Journal expands into a project-driven knowledge hub
Ever since its launch, RIO had been devised as the ultimate scholarly venue to share the early, intermediate and final results of a research project. While collections at the journal had already been put in good use, we still had what to add, so that we could provide a one-stop place for consortia to permanently store their outputs and make them easily discoverable and accessible long after their project had concluded.
With the upgraded collections, their owners received the oppotunity to also add various research publications – including scholarly articles published elsewhere, author-formatted documents and preprints. In the former case, the article is visualised within the collection at RIO via a link to its original source, while in the latter, it is submitted and published via ARPHA Preprints.
2021b: Pensoft becomes a coordinator of the BiCIKL project
Over the years, we have been partnering with many like-minded innovators and their institutions from across the natural science community. Surely, we hadn’t successfully developed all those technologies and workflows without their invaluable feedback and collaborations.
In 2021, our shared passion and vision about the future of research data availability and usage culminated in the project BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library), which was granted funding by the European Commission and will run until April 2024.
Within BiCIKL, our team of 14 European institutions are deploying and improving our own and partnering infrastructures to bridge gaps between each other’s biodiversity data types and classes with the ultimate goal to provide flawless access to data across all stages of the research cycle. By the end of the project, together we will have created the first-of-its-kind Biodiversity Knowledge Hub, where a researcher will be able to retrieve a full set of linked and open biodiversity data.
Naturally, being a coordinator of such a huge endeavour towards revolutionising biodiversity science is a great honour by itself.
For us, though, this project has a special place in our hearts, as it perfectly resonates with the very reason why we are here: publishing and sharing science in the most efficient and user-friendly manner.