Two red-tailed coral snakes have been observed competing over a caecilian in the first documented wild case of kleptoparasitism within the family Elapidae.
Kleptoparasitism, or food theft, is a well-documented behaviour in many animal species but is seldom reported among snakes in natural habitats.
Two Micrurusmipartitus snakes tugging prey in opposite directions. Credit: Henrik Bringsøe and Niels Poul Dreyer.
The observation, detailed in a recent study published in the open-access journal Herpetozoa by Henrik Bringsøe and Niels Poul Dreyer, showcases the two Micrurus mipartitus snakes engaging in a tug of war over the limbless amphibian.
Elapid snakes are venomous and among the deadliest serpents in the world. There are more than 400 species comprising a very diverse group of snakes such as mambas, cobras, kraits, taipans, tiger snakes, death adders, sea snakes and coral snakes.
The losing snake biting the body of the winning snake. Credit: Henrik Bringsøe and Niels Poul Dreyer.
The battle occurred in the dense rainforests of Valle del Cauca, western Colombia. Surprisingly, in the tussle, one snake also bit the body of the other. However, the researchers suggest this was likely accidental.
After 17 minutes of observation, the losing coral snake released its bite-hold on the caecilian. The winner then moved away from the losing snake which did not follow.
More footage of the battle. Credit: Henrik Bringsøe and Niels Poul Dreyer.
The study suggests that while such behaviours may be more common in captivity due to controlled environments, their occurrence in nature has been largely underreported, likely due to the elusive nature of these reptiles and the challenges of observing them in their natural habitats.
“Snakes in captivity do that often when only one prey is offered in a terrarium with two or more snakes. But it is rather surprising that it has not been observed more frequently in the wild.”
Henrik Bringsøe, lead author.
This case sheds light on the coral snake interactions with prey species. Caecilians, such as the one in this study, have shown remarkable adaptations such as toxin resistance and increased mucus production.
Henrik Bringsøe previously recorded snake feeding behaviour that was entirely new to science. Check out his guest blog post on the snakes that disembowel and feed on the organs of living toads.
Snake eating the organs of a toad. Credit: Winai Suthanthangjai.
Original source:
Bringsøe H, Dreyer NP (2024) Kleptoparasitism in Micrurus mipartitus (Squamata, Elapidae) competing for the same Caecilia sp. (Gymnophiona, Caeciliidae) in western Colombia. Herpetozoa 37: 77-84. https://doi.org/10.3897/herpetozoa.37.e112716
In 2023, the world of biodiversity saw some amazing discoveries . Our taxonomy journals published hundreds of new species, so selecting a Top Ten was tough, but here we go – get to know these beautiful new species, and maybe think about all the amazing diversity that still remains unexplored on our planet.
10. The walking leaf
It’s very often that undescribed species hide in plain sight for years, but it’s easy to understand why when they look like that! Leaf insects look confusingly similar to leaves – this sophisticated camouflage provides excellent protection from predators, but also presents a challenge to researchers.
“There are around 3,500 known species of stick and leaf insects and there are currently just over 100 described species of leaf insect,” researcher Dr Sven Bradler says. This is why when Phyllium ortizi and six other leaf insect species were found, it made for a really special discovery.
Lime-green in colour, Phyllium ortizi is so far only known from Mindanao Island, Philippines.
The Eastern Forest Hedgehog (Mesechinus orientalis) was discovered in southwestern China. It is a small-bodied hedgehog, smaller than most of the other species in its genus, its spines as short as 1.8-2 cm. It has a brown nose, with black whiskers that shorten towards the nose.
The species is currently known from southern Anhui and northwestern Zhejiang, where it lives in scrubland and subtropical broad-leaf evergreen forests at elevations from 30 to 700 m.
The researchers found out that genus Mesechinus, to which the new species belongs, dates back to the early Pleistocene and started appearing around 1.71 million years ago, while M. Orientalis diverged from its congeners some 1.1 million years ago.
Published in ZooKeys.
8. The bumpy salamander
Tylototriton zaimengwas found in the eponymous Zaimeng lake in Manipur, India. It is a medium-sized salamander has a massive wide head that could take up as much as a quarter of its total length. Its most distinctive feature are the knob-like warts along its body.
The salamander has an earthy-brown body with orange markings along its head and orange-brown warts down its back and sides. Its tail fades from brown at the base to yellow-orange at the tip.
#NewSpecies! New crocodile newt from India just snuck in:
An unexpected discovery, this new treefrog species was found in the Amazon lowlands of central Peru. The research team, led by Germán Chávez, was surprised that a new species could be hiding in plain sight in an otherwise well-explored part of the Amazon. No matter how many times they returned to the site, they only found two specimens, which made its scientific description challenging.
Its name, Scinax pyroinguinis, literally means “groins of fire”. It is a reference to the orange, flame-like pattern on the groins, thighs and shanks, but also to the wildfires in the area where it was found, which are a serious threat to its habitat.
Pinguicula ombrophila is part of the butterwort family, a group of insectivorous flowering plants consisting of around 115 species. Its leaves have a sticky texture, enabling it to capture and digest small insects.
For carnivorous plants, insects can be an additional source of nutrients to help them compensate the nutrient deficiency of the substrate they’re growing in. This gives them a competitive advantage over other plants and enables them to thrive in challenging habitats.
While the majority of butterworts are found in the northern hemisphere, this species was discovered in the elevated regions of southern Ecuador, near the Peru border. The research team found it on a nearly vertical rock face at 2,900 metres. Its name means “rain-loving butterwort”, highlighting the plant’s preference for very wet conditions.
Sinocyclocheilus longicornus(from the Latin words “longus”, meaning long, and “cornu”, meaning horn) comes from Southern China. It is only known from a dark vertical cave at an elevation of 2,276 m in the province of Guizhou. It is around 10-15 centimeters long and lacks pigmentation in its scales, which gives it it a ghostly whitish appearance. Since its eyes are small and probably not much help in a completely dark environment, it relies on barbels that look like tiny whiskers to feel its way around.
The researchers that found it are not quite sure what its “horn” is used for, but it might have something to do with navigating its way in the dark and dreary environment it inhabits.
Sinocyclocheilus longicornus is also featured in the SHOALS report on freshwater fish species described in 2023.
Sibon irmelindicaprioae was described as a new species together with four more tree-dwelling snake species from jungles of Ecuador, Colombia, and Panama. They all belong to Dipsadinae —a subfamily of snakes found in North and South America.
Also known as DiCaprio’s snail-eating snake, this species was named after actor and film producer Leonardo DiCaprio’s mother, Irmelin DiCaprio. The actor himself chose the name to honour his mother and raise awareness about the threats these snakes face.
Its habitat in Panama is affected by large-scale copper mining. The open-pit mines, some of them visible from space, make the areas uninhabitable for snail-eating snakes.
“These new species of snake are just the tip of the iceberg in terms of new species discoveries in this region, but if illegal mining continues at this rate, there may not be an opportunity to make any future discoveries,” says Alejandro Arteaga, who led the study to describe them.
Published in ZooKeys.
3. The Tolkien frog
You probably guessed it by now – this stream frog from the Ecuadorian Andes was named after J.R.R. Tolkien, the author of The Hobbit and The Lord of the Rings.
At about 66 millimeters (2.5 inches) long, Hyloscirtus tolkieniis tiny enough to fit in the palm of your hand, but that doesn’t stop it from being simply stunning. With pale pink eyes and gold-speckled toes, it looks like it came straight out of Middle-earth. It was found at an elevation of 3190 meters in Río Negro-Sopladora National Park, a protected area of páramo and cloud forests.
I'm at a nerd convention today so here's the nerdiest frog I could find. Frog of the day is Hyloscirtus tolkieni, named for J. R. R. Tolkien. Photo is from the paper describing its recent discovery! https://t.co/DsQmzm7Np2pic.twitter.com/fpKBST6Uux
— LadyLasergun | Teatuber (@LadyLasergun) August 3, 2023
“The new species of frog has amazing colours, and it would seem that it lives in a universe of fantasies, like those created by Tolkien. The truth is that the tropical Andes are magical ecosystems where some of the most wonderful species of flora, funga, and fauna in the world are present. Unfortunately, few areas are well protected from the negative impacts caused by humans. Deforestation, unsustainable agricultural expansion, mining, invasive species, and climate changes are seriously affecting Andean biodiversity”, said Diego F. Cisneros-Heredia, one of the researchers behind this discovery.
Published in ZooKeys.
2. The enigmatic Nautilus
2023 was a great year for nautilus biodiversity: three species were described as new to science, including Nautilus samoaensis, which you see here. Like its name tells you, it was found off the coast of American Samoa.
Studying nautilus diversity is no easy feat – with setting spiky traps, hauling them over on board, and, eventually, burping nautiluses, it is surely a memorable experience.
Judging by the fossil record, nautiloids were once quite plentiful throughout the oceans. Today, however, they are represented by just a handful of species.
In addition, these fragile animals remain threatened by wildlife trade as they are hunted for their shells, which according to Mongabay can sell for up to about $1,000 each on the black market.
Found in Thailand’s Phang-Nga province, Chilobrachys natanicharum features an enchanting phenomenon: a neon blue-purple coloration that gives it a unique look.
There is no blue pigment in this tarantula’s body: the secret behind its striking color comes from the unique structure of its hair, which incorporates nanostructures that manipulate light in an effect that creates the blue appearance. Depending on the light, it can also appear violet.
Before it was described as a new species, Chilobrachys natanicharum was actually known to experts from the commercial tarantula trade market as “Chilobrachys sp. Electric Blue Tarantula,” but this is the first time that it’s discovered in its natural habitat.
Its name, in fact, resulted from an auction campaign, the proceeds from the auction have been channeled to bolster the education of Lahu children in Thailand and to aid impoverished cancer patients.
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.
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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.
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.
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.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
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.
By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.
This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.
All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.
“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”
comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”
adds Yvonne Campfens, Executive Director of the OA Switchboard.
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About the OA Switchboard:
A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.
About Pensoft:
Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.
All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.
Herpetozoa, the peer-reviewed scientific journal of the Austrian Herpetological Society, renewed its contract with Pensoft, re-signing with the scholarly publisher for another five years. Published since 1988, the journal offers a venue for research articles, short contributions and reviews dealing with all aspects of the study of amphibians and reptiles.
Herpetozoa, thepeer-reviewed scientific journal of the Austrian Herpetological Society, renewed its contract with Pensoft, re-signing with the scholarly publisher for another five years. Published since 1988, the journal offers a venue for research articles, short contributions and reviews dealing with all aspects of the study of amphibians and reptiles.
Enticed by the opportunities that open access publishing offers, and looking to improve its visibility, Herpetozoa first came to Pensoft in 2019. The move equipped the journal with abrand new website and a full suite of publishing services tailored to the needs of biodiversity-themed academic publications available from ARPHA, Pensoft’s self-developed publishing platform.
In ARPHA’s fast-track publishing system, each manuscript is carried through all stages, from submission and reviewing to dissemination and archiving, without ever leaving the platform’s collaboration-friendly online environment. In addition, semantic enhancements, automated data export to aggregators, web-service integrations with major indexing databases, and a variety of publishing formats ensure that all articles are easy to find, access, and use by both humans and machines.
The journal also makes use of ARPHA Preprints, another service developed by Pensoft to streamline public access to the latest scientific findings. The platform allows authors to submit a preprint in a matter of seconds along with their manuscript, with no need to upload any additional files. Following a quick in-house screening, the preprint is then made available on ARPHA Preprints in a few days’ time. Once the associated paper is published, a two-way link between the article and the preprint is established via CrossRef.
In the past three years, we saw Herpetozoa publish some quite peculiar discoveries that were quick to attract the attention of the global media. Such was the case of a set of first-of-their-kind observations of kukri snakes gutting toads and eating their organs while still alive. At the same time, the journal doesn’t fail to bring public attention to urgent conservation and biodiversity loss issues like reptile poaching in Pakistan, as well as innovative methods to monitor delicate amphibians in a non-invasive manner.
