Researchers who captured footage of dog attacks on endangered mountain tapirs in Colombia are calling for action to protect threatened wildlife.
Using camera traps, a team from WILD Campo Silvestre, the Tiger Cats Conservation Initiative, and the Fundación Caipora captured images of two attacks in the Campoalegre Soil Conservation District, Santa Rosa de Cabal in a period of two months.
Photographic evidence of domestic dogs chasing mountain tapirs in a private protected area of the Central Andes of Colombia. Credit: Cepeda-Duque et al.
The cameras caught domestic dogs (Canis lupus familiaris) chasing and attacking mountain tapirs (Tapirus pinchaque) in a protected area of the Central Andes. These images were subsequently published in a research paper published by the open-access journal, Neotropical Biology and Conservation.
The study offers insights into the impact of domestic dogs on wildlife, particularly on species of conservation concern such as the mountain tapir. The authors highlight the urgent need for population management and control of domestic dogs inside and around protected areas.
Area surveyed by camera traps that detected the two events of dogs mountain tapirs in the private natural reserve. Credit: Cepeda-Duque et al.
Conservationists recently implemented measures such as neutering and vaccination programs for stray and owned dogs in the vicinity of natural reserves to protect the threatened clouded tiger cat (Leopardus pardinoides) in the region. The research team call for these measures to be extended to WILD Campo Alegre and surrounding lands.
Campoalegre Soil Conservation District, Santa Rosa de Cabal. Credit: Camilo Botero.
“Domestic dog incursion into protected areas is a global threat to wildlife that is difficult to mitigate because of the inherent social dilemma of controlling dog populations,” says Juan Camilo Cepeda-Duque, lead author of the study.
“Dogs can contribute to the extinction of vertebrate species, can imbalance the trophic dynamics amongst predator guilds and even have the potential to collapse entire ecological communities,” he continues.
The mountain tapir is an emblematic herbivore of the Andean cloud forest, globally classified as ‘Endangered’ according to the IUCN Red List due to habitat loss and poaching. The presence and aggressive behaviour of domestic dogs not only threaten the physical wellbeing of these tapirs but also their reproductive performance, foraging efficiency, and overall population health due to increased stress, potential for disease transmission, and alterations in habitat use.
The research team highlight that their observations are not isolated cases, as locals previously reported the same dogs chasing and attacking mountain tapirs and cattle. The conservationists are also concerned that they detected no juvenile mountain tapirs in the survey.
Study authors Juan Camilo Cepeda Duque (left) and Eduven Arango Correa (right) on site. Credit: Camilo Botero.
The NGO WILD Nature Foundation has established a new protected area in the northern extreme of the Campoalegre Soil Conservation District, with the target of protecting the habitat of endangered mountain tapirs and the last remnant populations of the fuerte’s parrot (Hapalopsittaca fuertesi) in the region. Currently, the reserve is carrying out an unprecedented restoration program, planting thousands of trees to recover the land once cleared for the establishment of cattle ranching.
Original source
Cepeda-Duque JC, Arango-Correa E, Frimodt-Møller C, Lizcano DJ (2024) Howling shadows: First report of domestic dog attacks on globally threatened mountain tapirs in high Andean cloud forests of Colombia. Neotropical Biology and Conservation 19: 25-33. https://doi.org/10.3897/neotropical.19.e117437
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The city of Cambridge and the Wellcome Campus hosted the Final General Assembly of the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library): a 36-month endeavour that saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. Consortium members who could not attend the meeting in Cambridge joined the meeting remotely.
After a welcome cocktail reception on Monday evening at Hilton Cambridge City Centre, on Tuesday, the consortium made an early start with a recap of BiCIKL’s key milestones and outputs from the last three years. All Work Package leaders had their own timeslot to discuss the results of their collaborations.
They all agreed that the Biodiversity Knowledge Hub – the one-stop portal for understanding the complex – yet increasingly interconnected landscape of biodiversity research infrastructures – is likely the flagship outcome of BiCIKL.
Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers at the BiCIKL’s third and final General Assembly in Cambridge, United Kingdom.
In the afternoon, the participants focused on the services developed under BiCIKL. Amongst the many services resulting from the project some were not originally planned. Rather those were the ‘natural’ products of the dialogue and collaboration that flourished within the consortium throughout the project. “A symptom of passion,” said Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers.
An excellent example of one such service is what the partners call the “Biodiversity PMC”, which brings together biodiversity literature from thousands of scholarly journals and over 500,000 taxonomic treatments, in addition to the biomedical content available from NIH’s PubMed Central, into the SIB Literature Services (SIBiLS) database. What’s more, users at SIBiLS – be it human or AI – can now use advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions. Read more about the “Biodiversity PMC” in its recent official announcement.
Far from being the only one, the “Biodiversity PMC” is in good company: from the blockchain-based technology of LifeBlock to the curation of the DNA sequences by PlutoF, the BiCIKL project consortium takes pride in having developed twelve services dedicated to FAIR and linked ready-to-use biodiversity data.
On Wednesday, the consortium focused on BiCIKL’s activities from the Transnational and Virtual Access Pillar, which included both presentations by each open call leader and VA leader, as well as open discussions and a recap of what the teams have learnt from these experiences.
A panel discussion took place on Thursday as part of an open event, where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus.
Thursday was dedicated to an open event where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus. You can find the agenda on BiCIKL’s website.
After 36 months of action, the BiCIKL project will officially end in April 2024, but does it mean that all will be done and dusted come May 2024? Certainly not, point out the partners.
To ensure that the Biodiversity Knowledge Hub will not only continue to exist but will not cease to grow in both use and participation, the one-stop portal will remain under the maintenance of LifeWatch ERIC.
In conclusion, we could say that an appropriate payoff for the project is “Stick together!” as put by BiCIKL’s Joint Research Activity Leader Dr. Quentin Groom.
Final words at the third and last General Assembly of the BiCIKL project.
You can find highlights from the BiCIKL General Assembly meeting on X via the #BiCIKL_H2020 hashtag (in association with #Cambridge and #finalGA)
All research outputs, including the approved grant proposal, policy briefs, guidelines papers and research articles associated with the project, remain openly accessible from the BiCIKL project outcomes collection in RIO Journal: https://doi.org/10.3897/rio.coll.105.
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.
For the Pensoft team, September 2023 was a busy and exciting month filled with conferences. Travelling across Europe, they promoted journals, connected with the scientific community, and rewarded exceptional research with free article publications.
Let’s take a look back at all the events of the past month.
Pensoft representatives Mrs. Boriana Ovcharova and Mrs. Anna Sapundzhieva, ready to greet attendees in the sun.
The conference looked at evolutionary adaptations from the perspective of behavioural ecology, reproduction biology, genetics, physiology, as well as nature conservation. It particularly focused on the pressing issues of wildlife research and species conservation in the context of global environmental change. Most of the ≈100 participants were young scientists from more than 30 countries.
The Pensoft team greeted fellow attendees with an exhibition stand and presented the conservation and ecology-focused journals Neobiota, Nature Conservation, One Ecosystem, and Biodiversity Data Journal. Pensoft also advocated for EuropaBon, who are designing an EU-wide framework for monitoring biodiversity and ecosystem services, and REST-COAST, whose mission is to provide the tools to restore environmental degradation of rivers and coasts. Within both European-funded initiatives, Pensoft is a key dissemination partner that contributes expertise in science communication, scholarly publishing, and the development of digital tools and platforms.
Joao Pedro Meireles posing with his Best Poster award.
Pensoft presented Joao Pedro Meireles from Utrecht University with the Best Poster Award for his research on pair compatibility in okapis, entitling him to a free publication in one of Pensoft’s open-access journals.
“My study looked at pair compatibility in the zoo breeding programme of Okapi. During breeding introductions, sometimes the male becomes aggressive towards the female and we decided to investigate the potential factors. We ran a survey among all zoos that house the species in Europe and we found that differences in husbandry were linked to the aggressiveness performed by the males.”
Joao Pedro Meireles, Utrecht University
GfÖ Annual Meeting 2023
From the 12th to 16th of September, the German Centre for Integrative Biodiversity Research hosted the 52nd Annual Meeting of the Ecological Society of Germany, Austria and Switzerlandin Leipzig, Germany. The meeting welcomed more than 1,100 participants from around the world, including scientists, policymakers, educators, and environmental enthusiasts.
This year’s meeting was held with the theme: “The future of biodiversity – overcoming barriers of taxa, realms and scales.” There was a particular emphasis on future challenges and opportunities facing biodiversity, and how to address and manage these in an interdisciplinary and integrative way.
Mrs. Boriana Ovcharova (Pensoft) with Neobiota Editor-in-Chief Prof. Dr. Ingolf Kühn.
Conference participants were welcomed at the Pensoft stand, where they could learn more about the projects EuropaBon and SELINA, which deal with biodiversity, ecosystem and natural capital topics.
Also in Leipzig, the European Conference on Ecological Modellingtook place between the 4th and 8th of September. The event focused on the transformation of how societies deal with natural resources in a world where biodiversity and ecosystem services are at high risk.
The ECEM 2023 continued a series of conferences launched by the European chapter of ISEM, the International Society for Ecological Modelling. ISEM promotes the international exchange of ideas, scientific results, and general knowledge in the areas of systems’ analysis and simulations in ecology, and the application of ecological modelling for natural resource management.
📢Shutout to all attending the #ECEM23@ECEM_2023#ecological#modelling conference TODAY in Leipzig! Make sure to visit the poster session during lunch & find about the unique article types welcome to our #journal! 💡They intend to disseminate models PRIOR TO implementation! https://t.co/dUVskYFK11
— Food & Ecological Systems Modelling Journal, FESMJ (@FESMJournal) September 5, 2023
The Bundesinstitut für Risikobewertung team presented a poster on the Formal Model format and potential new MiDox formats, unique publication types that can be submitted to Pensoft’s Food and Ecological Modelling Journal.
118th Congress of the Italian Botanical Society
Speakers at the 118th Congress of the Italian Botanical Society.
Pensoft was proud to sponsor the 118th Congress of the Italian Botanical Society, which took place in Pisa, Italy from the 13th to 16th of September. Experts in various fields of Botany gathered to share their research on the following topics:
Journals promoted by Pensoft at the 94th Annual Meeting of the Paläontologische Gesellschaft.
Summer may be well and truly over, but as a new academic year begins, Pensoft looks forward to attending more conferences, rewarding more incredible research, and connecting with more of the scientific community. Thank you to everyone who contributed to or engaged with Pensoft’s open-access journals this year, and here’s to a successful final quarter of 2023.
Diversity and Wildlife Management: The legacy of PPG Biologia Unisinos was edited by former professors and students of PPG Biologia Unisinos, and features eight articles focused on the Neotropical region. Each study was conducted by the research teams of the program, or was only made possible with their help. It serves as a testament to the importance of the program.
On 21 July 2022, Unisinos, a private institution in southern Brazil, announced that it would discontinue 12 of its postgraduate programs, including PPG Biologia Unisinos. The program specialised in diversity and wildlife management and was the birthplace of the journal Neotropical Biology and Conservation in 2006.
Cover image for Diversity and Wildlife Management: The legacy of PPG Biologia Unisinos.
The closure of the programs was explained by Unisinos as a measure to maintain the university’s financial stability. However, this decision is widely seen as a significant setback for Brazilian research. It has disrupted the work of many professors and graduate students and is expected to have a noticeable negative impact on Brazilian research in the coming years.
“PPG Biologia Unisinos was a resilient postgraduate program with amazing professors that always did their best to keep the high quality of their research even when facing adversities such as budget cuts.
“We hope that this special issue helps raise awareness on the importance of biological research and encourages researchers from other institutions to defend their programs and advocate for more investment in biological research.”
Piter Boll, Neotropical Biology and Conservation’s editor-in-chief and former student of PPG Biologia Unisinos
Notable research featured in the issue includes a review of the management effectiveness of nature conservation units in southern Brazil, and a paper discussing the consequences of the program’s closure.
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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.
Guest blog post by Cássio Cardoso Pereira, Gabriela França Fernandes, and Walisson Kenedy Siqueira
We are bombarded day and night with slot-machine invitations from journals, books, and events such as congresses and lectures. Predatory publishing has reached alarming levels in biology, which is why we published an editorial in the journal Neotropical Biology and Conservation to alert the community, show the modus operandi of these publishers, and pass on good practices so that researchers, especially beginners, can escape this trap.
Piggybacking on the open access movement, numerous predatory publishers have emerged in search of easy profits. These cybercriminals take advantage of the publish-or-perish culture without providing any information about their peer-review protocols, concerned not with the scientific, bibliographic, or ethical aspects of publishing, but with the money received from authors.
The number of predatory publishers has grown exponentially in recent years and spread across all areas of knowledge, including biology. It is a common practice of these journals, often with an equally fake editorial staff, to send electronic invitations to potential authors to publish articles. These invitations are often facilitated by initial screenings of the emails of corresponding authors available on the internet. The emailed invitations from the supposed editors often stress that the author’s work is sound and, since it has already gone through the scrutiny of the editorial board, requires only the payment of a fee to publish it, with no need for further peer review.
Invitations to join the editorial board of these journals are also frequent, mostly intended to take advantage of the scientists’ prestige. Instead of editing articles, these invited editors are used as poster boys, i.e., they have their names published on the journal’s website, thus attracting unsuspecting authors to submit their manuscripts.
These journals are generally not included in the directory of open access journals (DOAJ) and are not indexed in the main bibliometric databases, such as Google Scholar, SciELO, Scopus, and Web of Science, for the simple reason that they do not meet their inclusion criteria. The websites of these journals often have little information about the editorial board, have a fake International Standard Serial Number (ISSN), lack transparency regarding their scope, provide no indication of a policy of retraction, have no transparency regarding copyright transfer, and provide very vague contact information, often omitting the address of the journal’s office.
In addition to papers, there are also invitations to publish books and book chapters with fake International Standard Book Numbers and dubious editorial boards. There is also a flood of invitations to predatory meetings, such as online conferences, symposia, workshops, and lectures. These often have websites that are equally confusing and never linked to a university or a postgraduate program. Above all, one should consult advisors, supervisors, or senior colleagues about the invitation and the sender’s academic reputation. In any case, one must pay attention not only to the citation metrics but also, mainly, to their editorial board, ISSN, ISBN, contact information, and relationships with recognized institutions.
When we analyze the impacts of predatory publishing on the scientific community, the worst problems are:
the dissemination of erroneous information about scientific problems of interest
the facilitation of plagiarism
the waste of public resources intended for publication
the appointment of researchers at universities and research institutes based on curricula full of doubtful publications, generating negative cascading effects that undermine higher education as a whole.
The damage done to society can be even worse. Governments, large companies, and decision-makers can be misled by false information, resulting in attitudes that undermine responses to major human problems such as climate change, biodiversity, and pandemics.
Efforts to fight predatory publishers require collaboration and support at higher levels. Governments need to create regulatory agencies that carefully and systematically evaluate the activities carried out by scientific journals. Science funding agencies should require that publication fees be paid only to publishers that adhere to an internationally recognized set of transparency and ethical rules. We need to discuss our values and incentives in the academic community, so we can start prioritizing quality over quantity. This would provide a reference point for research, help design coherent interventions, and improve information and public policy in favor of society and the environment.
Reference:
Pereira CC, Mello MAR, Negreiros D, Figueiredo JCG, Kenedy-Siqueira W, Maia LR, Fernandes S, Fernandes GFC, Ponce de Leon A, Ashworth L, Oki Y, de Castro GC, Aguilar R, Fearnside PM, Fernandes GW (2023) Beware of scientific scams! Hints to avoid predatory publishing in biological journals. Neotropical Biology and Conservation 18(2): 97-105. https://doi.org/10.3897/neotropical.18.e108887
Readers at some of the journals published by Pensoft, who have downloaded/printed a publication or ordered a physical copy of a journal issue over the last few weeks, might be in for a surprise concerning the layout of the PDF format of the articles.
Research papers published in ZooKeys demonstrating the former (left) and the current (right) article layout seen in the PDF format.
Even though it’s been years since online publishing has become the norm in how we are consuming information – including scientific publications – we understand that academia is still very much fond of traditional, often paper-based, article layout format: the one you use when accessing a PDF file or a print copy, rather than directly scrolling down through the HTML version of the article.
Even if today large orders of printed volumes from overseas are the exception, rather than the rule, we know we have readers of ours who regularly print manuscripts at home or savе them on their devices. Trends like this have already led to many journals first abandoning the physical- for digital-first, then transitioning to digital-only publication format.
Meanwhile, it is true that needs and demands have fundamentally changed in recent times.
As we speak, readers are accessing PDF files from much higher-quality desktops, in order to skim through as much content as possible.
In the meantime, authors are relying on greater-quality cameras to document their discoveries, while using advanced computational tools capable of generating and analysing extra layers of precise data. While producing more exhaustive research, however, it is also of key importance that their manuscripts are processed and published as rapidly as possible.
So, let’s run through the updates and give you our reasoning for their added value to readers and authors.
Revised opening page
One of the major changes is the one to the format of the first page. By leaving some blank space on the left, we found a dedicated place for important article metadata, i.e. academic editor, date of manuscript submission / acceptance / publication, citation details and licence. As a result, we “cleaned up” the upper part of the page, so that it can better highlight the authors and their affiliations.
Bottom line: The new layout provides a better structure to the opening page to let readers find key article metadata at a glance.
Expand as much – or as little – as comfortable
As you might know, journals published by Pensoft have been coming in different formats and sizes. Now, we have introduced the standard A4 page size, where the text is laid in a single column that has been slightly indented to the right, as seen above. Whenever a figure or a table is used in a manuscript, however, it is expanded onto the whole width of the page.
Before giving our reasons why, let’s see what were the specific problems that we address.
Case study 1
Some of our signature journals, including ZooKeys, PhytoKeys and MycoKeys, have become quite recognisable with their smaller-than-average B5 format, widely appreciated by people who would often be seen carrying around a copy during a conference or an international flight.
However, in recent times, authors began to embrace good practices in research like open sharing of data and code, which resulted in larger and more complex tables. Similarly, their pocket-sized cameras would capture much higher-resolution photos capable of revealing otherwise minute morphological characters. Smaller page size would also mean that often there would be pages between an in-text reference of a figure or a table and the visual itself.
So, here we faced an obvious question: shall we deprive their readers from all those detailed insights into the published studies?
Yet, the A4 format brought up another issue: the lines were too long for the eye comfort of their readers.
What they did was organise their pages into two-column format. While this sounds like a good and quite obvious decision, the format – best known from print newspapers – is pretty inconvenient when accessed digitally. Since the readers would like to zoom in on the PDF page or simply access the article on mobile, they will need to scroll up and down several times per page.
In addition, the production of a two-column text is technologically more challenging, which results in extra production time.
Bottom line: The new layout allows journals to not sacrifice image quality for text readability and vice versa. As a bonus, authors enjoy faster publication for their papers.
Simplified font
If you have a closer look at the PDF file, you would notice that print-ready papers have also switched to a more simplistic – yet easier to the eye – font. Again, the update corresponds to today’s digital-native user behaviour, where readers often access PDF files from devices of various resolutions and skim through the text, as opposed to studying its content in detail.
In fact, the change is hardly new, since the same font has long been utilised for the webpages (HTML format) of the publications across all journals.
Bottom line: The slightly rounder and simplified font prompts readability, thereby allowing for faster and increased consumption of content.
What’s the catch? How about characters and APCs?
While we have been receiving a lot of positive feedback from editors, authors and readers, there has been a concern that the updates would increase the publication charges, wherever these are estimated based on page numbers.
Having calculated the lines and characters in the new layout format, we would like to assure you that there is no increase in the numbers of characters or words between the former and current layout formats. In fact, due to the additional number of lines fitting in an A4 page as opposed to B5, authors might be even up for a deal.
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* At the time of the writing, the new paper layout has not been rolled out at all journals published by Pensoft. However, most of the editorial boards have already confirmed they would like to incorporate the update.
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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,”
