Category: Biodiversity Data Journal

How to ensure biodiversity data are FAIR, linked, open and future-proof?

Now concluded Horizon 2020-funded project BiCIKL shares lessons learned with policy-makers and research funders

Within the Biodiversity Community Integrated Knowledge Library (BiCIKL) project, 14 European institutions from ten countries, spent the last three years elaborating on services and high-tech digital tools, in order to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of various types of data about the world’s biodiversity. These types of data include peer-reviewed scientific literature, occurrence records, natural history collections, DNA data and more.

By ensuring all those data are readily available and efficiently interlinked to each other, the project consortium’s intention is to provide better tools to the scientific community, so that it can more rapidly and effectively study, assess, monitor and preserve Earth’s biological diversity in line with the objectives of the likes of the EU Biodiversity Strategy for 2030 and the European Green Deal. Their targets require openly available, precise and harmonised data to underpin the design of effective measures for restoration and conservation, reminds the BiCIKL consortium.

Since 2021, the project partners at BiCIKL have been working together to elaborate existing workflows and links, as well as create brand new ones, so that their data resources, platforms and tools can seamlessly communicate with each other, thereby taking the burden off the shoulders of scientists and letting them focus on their actual mission: paving the way to healthy and sustainable ecosystems across Europe and beyond.

New BiCIKL project to build a freeway between pieces of biodiversity knowledge

Now that the three-year project is officially over, the wider scientific community is yet to reap the fruits of the consortium’s efforts. In fact, the end of the BiCIKL project marks the actual beginning of a European- and global-wide revolution in the way biodiversity scientists access, use and produce data. It is time for the research community, as well as all actors involved in the study of biodiversity and the implementation of regulations necessary to protect and preserve it, to embrace the lessons learned, adopt the good practices identified and build on the knowledge in existence.

This is why amongst the BiCIKL’s major final research outputs, there are two Policy Briefs meant to summarise and highlight important recommendations addressed to key policy makers, research institutions and funders of research. After all, it is the regulatory bodies that are best equipped to share and implement best practices and guidelines.

Most recently, the BiCIKL consortium published two particularly important policy briefs, both addressed to the likes of the European Commission’s Directorate-General for Environment; the European Environment Agency; the Joint Research Centre; as well as science and policy interface platforms, such as the EU Biodiversity Platform; and also organisations and programmes, e.g. Biodiversa+ and EuropaBON, which are engaged in biodiversity monitoring, protection and restoration. The policy briefs are also to be of particular use to national research funds in the European Union.

One of the newly published policy briefs, titled “Uniting FAIR data through interlinked, machine-actionable infrastructures”, highlights the potential benefits derived from enhanced connectivity and interoperability among various types of biodiversity data. The publication includes a list of recommendations addressed to policy-makers, as well as nine key action points. Understandably, amongst the main themes are those of wider international cooperation; inclusivity and collaboration at scale; standardisation and bringing science and policy closer to industry. Another major outcome of the BiCIKL project: the Biodiversity Knowledge Hub portal is noted as central to many of these objectives and tasks in its role of a knowledge broker that will continue to be maintained and updated with additional FAIR data-compliant services as a living legacy of the collaborative efforts at BiCIKL.

The second policy brief, titled “Liberate the power of biodiversity literature as FAIR digital objects”, shares key actions that can liberate data published in non-machine actionable formats and non-interoperable platforms, so that those data can also be efficiently accessed and used; as well as ways to publish future data according to the best FAIR and linked data practices. The recommendations highlighted in the policy brief intend to support decision-making in Europe; expedite research by making biodiversity data immediately and globally accessible; provide curated data ready to use by AI applications; and bridge gaps in the life cycle of research data through digital-born data. Several new and innovative workflows, linkages and integrative mechanisms and services developed within BiCIKL are mentioned as key advancements created to access and disseminate data available from scientific literature. 

While all policy briefs and factsheets – both primarily targeted at non-expert decision-makers who play a central role in biodiversity research and conservation efforts – are openly and freely available on the project’s website, the most important contributions were published as permanent scientific records in a BiCIKL-branded dedicated collection in the peer-reviewed open-science journal Research Ideas and Outcomes (RIO). There, the policy briefs are provided as both a ready-to-print document (available as supplementary material) and an extensive academic publication.

Currently, the collection: “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” in the RIO journal contains 60 publications, including policy briefs, project reports, methods papers, conference abstracts, demonstrating and highlighting key milestones and project outcomes from along the BiCIKL’s journey in the last three years. The collection also features over 15 scientific publications authored by people not necessarily involved in BiCIKL, but whose research uses linked open data and tools created in BiCIKL. Their publications were published in a dedicated article collection in the Biodiversity Data Journal.

BiCIKL keeps on adding project outcomes in own collection in RIO Journal

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Visit the Biodiversity Community Integrated Knowledge Library (BiCIKL) project’s website at: https://bicikl-project.eu/.

Don’t forget to also explore the Biodiversity Knowledge Hub (BKH) for yourself at: https://biodiversityknowledgehub.eu/ and watch the BKH’s introduction video. 

Highlights from the BiCIKL project are also accessible on Twitter/X from the project’s hashtag: #BiCIKL_H2020 and handle: @BiCIKL_H2020.

BiCIKL project sums up outcomes and future prospects at a Final GA in Cambridge

A new 3D printable model of an entomological pinning block

Intended for widespread use by entomologists, the block is applicable to large entomological collections with individual specimen numbering.

Guest blog post by Ilia Vladimirov Gjonov

The proposed model of an entomological block is ready for printing on a standard 3D printer. In addition to the usual positioning of glue boards and labels along the Z-axis, the model also offers targeting devices that enable precise positioning of the entomological pin along the X- and Y-axes.

A scheme of a 3D-printable model of an entomological pinning block.
Dimensions of the entomological pinning block with metal rail.

The model is offered in two variants – one for immediate use after printing and another that requires the fabrication of an additional steel rail measuring 100 × 30 × 5 mm, against which the tip of the pin rests during positioning along the Z-axis. The rail is also used to increase the overall mass of the fixture. The overall dimensions of the device are 100 mm in length, 35 mm in width and 37 mm in height.

The proposed entomological block is intended for widespread use by entomologists, particularly those using insect glue boards. It is applicable to large entomological collections with individual specimen numbering and its use can ensure that entomological pins are positioned on the label so as not to disrupt the integrity of the number or barcode. It can also be modified to suit the needs of the user and can be sliced and printed directly on a 3D printer.

Methods paper:

Gjonov I, Hristozov A (2024) 3D printable model of an entomological pinning block, designed for precise positioning of entomological glue boards and labels. Biodiversity Data Journal 12: e121569. https://doi.org/10.3897/BDJ.12.e121569

Pensoft wishes “Happy 90th birthday!” to thrips expert Dr. Laurence Mound

To date, Dr. Laurence Mound is the most prolific thrips researcher in history and has made monumental contributions to the field.

Today, Pensoft celebrates one of its most distinguished editors and the world’s leading authority on thrips: Dr. Laurence Mound on the occasion of his 90th birthday.

Born in Willesden, London, on 22 April 1934, Dr. Mound is considered a world authority in the field. Having received his PhD from the University of London, he has been studying the biology and systematics of the order Thysanoptera for more than six decades. His academic recognitions include honorary membership at both the Royal and the Australian Entomological societies.

To date, Dr. Laurence Mound is the most prolific thrips researcher in history and has made monumental contributions to the field as the author of 500 publications, including landmark papers that have since shaped our understanding of the taxonomy and evolution of thrips. He has also published a number of books on thrip identification and control.

Having worked with admirable devotion and persistence to advance the knowledge of thrips on a global scale, Dr. Mound has described over 700 species and 100 genera. His studies have helped with species identifications in important pest groups, which in turn has had a pivotal role in the management of pests and the prevention of the establishment of new pest species.

One of the first-ever entomologists to join the ZooKeys editorial team, Mound has been the journal’s go-to editor for the order Thysanoptera for more than a decade. He oversaw the publication of 18 research papers at ZooKeys. He has also authored 11 articles in the journal, including especially valuable identification keys of different taxa from across the globe. He has also been one of the journal’s active reviewers.

Other journals published by Pensoft have also benefited from Mound’s invaluable scientific contributions. Over the years, the renowned thrips expert has also been an author, reviewer, and editor at Deutsche Entomologische Zeitschrift, Biodiversity Data Journal, Check List and Journal of Orthoptera Research.

“As a founder of ZooKeys, I’d like to specially congratulate Laurence on his 90th anniversary and personally thank him for his admirable involvement in our beloved journal. I cannot stress it enough how central dedicated and passionate scientists like him are to have a journal establish itself as a top-quality community-led resource of knowledge. As a fellow entomologist, I’d like to wish him health and good fortune for many years to come; and may the devotion and fascination you have invested in the field extend to each and every aspect of your life!”

says Prof. Dr. Lyubomir Penev, founder/CEO of Pensoft and founding editor of ZooKeys.

“As Editor-in-Chief of ZooKeys, I wish you a ‘Happy 90th birthday!’ and thank you for your dedication and support of the journal since its very early days,”

says Dr. Torsten Dikow, Editor-in-Chief at ZooKeys and research entomologist and curator at the Smithsonian National Museum of Natural History (USA).

“It was Laurence Mound who suggested my name to replace him as subject editor for Thysanoptera at ZooKeys five years ago. Since then, Laurence has actively continued to be a major contributor of both papers and reviews to the journal. It is an honour to share his friendship and to be able to continually receive his support, encouragement and guidance over the years. I would like to express my gratitude and wish an excellent birthday to this researcher who inspires all of us who study Thysanoptera and entomology in general,”

says Prof. Dr. Elison Lima, Adjunct professor at Universidade Federal do Piauí (Brazil) and fellow thrips expert.

“We are truly honoured to have been working with Laurence all these years! His passion and dedication have left a permanent mark on the field of entomology. We toast to the future success and happiness of a dear friend, editor, and author. May his work continue to inspire many more generations of entomologists and conservationists,”

adds Pensoft’s editorial team.

Fourteen years after the Gulf of Mexico oil spill, endemic fishes face an uncertain future

A study investigating the spill’s impact on endemic fish species suggests potential loss of biodiversity.

The 2010 Gulf of Mexico Deepwater Horizon was the largest accidental oil spill in history. With almost 100 million gallons (379 million liters) of oil combined with dispersants suggested to remain in the Gulf, it is one of the worst pollution events ever. More than a decade later, its long-term effects  are still not fully understood.

A ship sails among spilled oil in the Gulf of Mexico after the BP Deepwater Horizon oilspill disaster.
A ship sails among spilled oil in the Gulf of Mexico after the BP Deepwater Horizon oilspill disaster. Photo by Kris Krug shared under a CC BY-NC-SA 2.0 license.

In a new study, researchers from Louisiana State University and Tulane University examined the endemic Gulf of Mexico fish species that may have been most impacted by the oil spill to see how their distribution has changed over the years. To get their data, they studied museum specimens from natural history collections, looked at relevant literature, and combed biodiversity databases.

Lead author Prosanta Chakrabarty in the fish collections of the Louisiana State University Museum of Natural Science, where many specimens from the Gulf of Mexico are housed.
Lead author Prosanta Chakrabarty in the fish collections of the Louisiana State University Museum of Natural Science where many specimens from the Gulf of Mexico are housed. Photo credit: Eddy Perez, LSU

With 1541 fish species known from the region, and 78 endemic fish species, the Gulf of Mexico is one of the most biologically rich and resilient marine environments in the world, but how much of this diversity is still left intact?

The study found that 29 out of the Gulf’s 78 endemic fish species haven’t been reported in museum collections since 2010. The Yucatan killifish, for example, which is considered endangered, was last reported pre-spill, in 2005, off the Yucatán Peninsula.

Six of the non-reported species are considered of greatest concern, because their areas of distribution largely overlap with the affected area – although the authors note that their absence in the Gulf in recent years cannot automatically be attributed to the oil spill.

Jars of voucher specimens of fishes at the Louisiana State University Museum of Natural Science.
Jars of voucher specimens of fishes at the Louisiana State University Museum of Natural Science. Photo credit: Eddy Perez, LSU

“Understanding the impacts of catastrophic environmental events such as the 2010 Gulf of Mexico Oil Spill does not end when the wellhead is capped or when the last drops of oil cease to flow. The disaster only begins to end when the data no longer show impacts of the event. We are far from the beginning of the end for the Deepwater Horizon Oil Spill. Lingering chemicals, lost generations of wildlife and a continued ecosystem imbalance may all be factors that prevent an environment from rebounding from such cataclysmic events,” the authors note in their research article.

However, they also point out that nature’s ability to recover should not be overlooked.

“The Gulf of Mexico continues to face many challenges, from the Dead Zone, to climate change, loss of coast habitats and continued oil spills. Efforts like this report aim to bring attention to vulnerable species that continue to be impacted by human activities and to the unique endemic fauna of the region,” the researchers write in conclusion.

Research article:

Chakrabarty P, Sheehy AJ, Clute X, Cruz SB, Ballengée B (2024) Ten years later: An update on the status of collections of endemic Gulf of Mexico fishes put at risk by the 2010 Oil Spill. Biodiversity Data Journal 12: e113399. https://doi.org/10.3897/BDJ.12.e113399

Deciphering cyrillics: revealing the myxomycetes of Ukraine from invisible sources

A new study compiles over 150 years of research on Ukraine’s myxomycetes – amoebae that form fascinating fungi-like fruiting bodies.

Guest blog post by Iryna Yatsiuk

A graphic showing the occurrences of myxomycetes on a map of Ukraine.
Occurrences of myxomycetes in Ukraine from the present study.

Myxomycetes, or slime molds, despite their unassuming name, are fascinating organisms that play a crucial role in forest ecosystems. They live as single-cell amoebae in soil or all sorts of plant debris, where they feed on microscopic bacteria, algae, and fungi. However, when it is time to reproduce and disseminate, these tiny amoebae fuse with each other and form slimy, mobile structures – plasmodia. Plasmodia slowly but actively crawl on the substrate, and eventually transform into fungi-like fruiting bodies filled with spores. Both plasmodia and fruiting bodies are visible with the naked eye and can be easily found e.g. on decaying wood or on the forest floor.

Yellow slime mold on a tree trunk.
Fruiting bodies of slime mold on a tree trunk.
Plasmodium (left) and fruiting bodies (right) of the same species of a slime mold, with a difference of one day.

Myxomycetes are unusual in their life cycle and very eye-catching – if only one knows where to look for them. No wonder that they have attracted the attention of naturalists for centuries. On the territory of Ukraine, observations of myxomycetes first appeared in the first half of 19th century and have been occurring sporadically in the mycological literature ever since.

Slime mold.
‘Wasp nest’ slime mold – a common and widespread species of myxomycetes in Ukraine.

However, much valuable information about the myxomycetes of Ukraine before our study was in a “grey zone”. This includes undigitized historical books and articles published in languages such as Polish, French, or German. Furthermore, there is a significant body of proceedings of local conferences, articles in local journals, and reports produced by the employees of protected areas. Yet, many of these publications existed only in print and were written in the Cyrillic alphabet, so they remained difficult to discover, to access, or to work with.

A page of Maria Zelle's work “Materials for the myxomycete flora of Ukraine”.
An example of an “invisible” literature source, a page from Maria Zelle “Materials for the myxomycete flora of Ukraine”, 1925.

Within this study, published in Biodiversity Data Journal, we aimed to summarize all published research on myxomycetes of Ukraine, which spans over 150 years, and make the data, as well as the literature behind the data, open and easy to use. For this, we collected and mined 91 publications on this topic, spanning the years 1842 to 2023. As the result, we extracted over 5000 occurrences of myxomycetes that belong to 331 species. The produced datasets we published on GBIF, and the major part of the literature sources on the platform Zenodo.org in open access.

Datasets produced by this study available on GBIF.
A group of researchers posing for a picture.
Leaders of the BioData project with future Ukrainian mentors.

With this initiative, we aimed to open to the wider audience and digitally preserve some part of the biodiversity data heritage of Ukraine that is currently under threat of destruction.

This study was substantially driven by the BioDATA project, which helped a lot in developing biodiversity data management skills in our team.

Research article:

Yatsiuk I, Leshchenko Y, Viunnyk V, Leontyev DV (2024) The comprehensive checklist of myxomycetes of Ukraine, based on extended occurrence and reference datasets. Biodiversity Data Journal 12: e120891. https://doi.org/10.3897/BDJ.12.e120891

Potamophylax kosovaensis, a new insect species from Kosovo that is already endangered

The country’s natural wealth is under threat by manmade pressures such as water pollution, littering, and the construction of hydropower plants.

Over the last few years, professor Halil Ibrahimi from Kosovo and his team have described several new species of aquatic insects revered as bioindicators of freshwater ecosystems. However, the celebration of these discoveries is tempered by alarming concerns: the newfound species are often already considered endangered, as per the criteria set forth by the International Union for Conservation of Nature (IUCN), as soon as they are described. This classification underscores the urgent need for conservation efforts to safeguard their existence.

The research team just discovered a new species, named Potamophylax kosovaensis, in the spring area of the Llap River, nestled within the Ibër River Basin. The region, known for its ecological significance, serves as a critical habitat for numerous aquatic organisms like newly discovered insect species.

The caddisfly Potamophylax kosovaensis.
Potamophylax kosovaensis.

Unfortunately, these freshwater insects are facing unprecedented threats in Kosovo and the broader Balkans region. Anthropogenic pressures, such as water pollution, littering, and the construction of hydropower plants, pose imminent risks to their survival. The degradation of their habitats not only jeopardizes their existence, but also undermines the health and integrity of entire freshwater ecosystems.

Spring area of the Llap river in Kosovo.
Spring area of the Llap river, from where the new species, Potamophylax kosovaensis was found.

Professor Ibrahimi emphasizes on the importance of urgent action to mitigate these threats and conserve this delicate balance of freshwater biodiversity. “The discovery of Potamophylax kosovaensis serves as a stark reminder of the fragility of our freshwater ecosystems,” he states. “We must prioritize efforts to protect these habitats and the invaluable species they harbor.”

A polluted waterway in Kosovo.
A polluted natural area in Kosovo.
Anthropogenic pressures in freshwater ecosystems in Kosovo endangering rich aquatic biodiversity.

The study was financed by the Integrated Water Resource Management in Kosovo (IWRM-K) and was conducted in the Laboratory of Zoology-Department of Biology of the University of Prishtina. It was published in the open-access, peer-reviewed Biodiversity Data Journal.

Research article:

Ibrahimi H, Bilalli A, Geci D, Grapci Kotori L (2024) Potamophylax kosovaensis sp. nov. (Trichoptera, Limnephilidae), a new species of the Potamophylax winneguthi species cluster from the Ibër River Basin in Kosovo. Biodiversity Data Journal 12: e121454. https://doi.org/10.3897/BDJ.12.e121454

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Pensoft took a BiCIKL ride to Naturalis to report on a 3-year endeavour towards FAIR data

Three years ago, the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data.

Leiden – also known as the ‘City of Keys’ and the ‘City of Discoveries’ – was aptly chosen to host the third Empowering Biodiversity Research (EBR III) conference. The two-day conference – this time focusing on the utilisation of biodiversity data as a vehicle for biodiversity research to reach to Policy – was held in a no less fitting locality: the Naturalis Biodiversity Center. 

On 25th and 26th March 2024, the delegates got the chance to learn more about the latest discoveries, trends and innovations from scientists, as well as various stakeholders, including representatives of policy-making bodies, research institutions and infrastructures. The conference also ran a poster session and a Biodiversity Informatics market, where scientists, research teams, project consortia, and providers of biodiversity research-related services and tools could showcase their work and meet like-minded professionals.

BiCIKL stops at the Naturalis Biodiversity Center

The main outcome of the BiCIKL project: the Biodiversity Knowledge Hub, a one-stop knowledge portal to interlinked and machine-readable FAIR data.

The famous for its bicycle friendliness country also made a suitable stop for BiCIKL (an acronym for the Biodiversity Community Integrated Knowledge Library): a project funded under the European Commission’s Horizon 2020 programme that aimed at triggering a culture change in the way users access, (re)use, publish and share biodiversity data. To do this, the BiCIKL consortium set off on a 3-year journey to build on the existing biodiversity data infrastructures, workflows, standards and the linkages between them.

Many of the people who have been involved in the project over the last three years could be seen all around the beautiful venue. Above all, Naturalis is itself one of the partnering institutions at BiCIKL. Then, on Tuesday, on behalf of the BiCIKL consortium and the project’s coordinator: the scientific publisher and technology innovator: Pensoft, Iva Boyadzhieva presented the work done within the project one month ahead of its official conclusion at the end of April.

As she talked about the way the BiCIKL consortium took to traverse obstacles to wider use and adoption of FAIR and linked biodiversity data, she focused on BiCIKL’s main outcome: the Biodiversity Knowledge Hub (BKH).

Key results from the BiCIKL project three years into its existence presented by Pensoft’s Iva Boyadzhieva at the EBR III conference.

Intended to act as a knowledge broker for users who wish to navigate and access sources of open and FAIR biodiversity data, guidelines, tools and services, in practicality, the BKH is a one-stop portal for understanding the complex but increasingly interconnected landscape of biodiversity research infrastructures in Europe and beyond. It collates information, guidelines, recommendations and best practices in usage of FAIR and linked biodiversity data, as well as a continuously expanded catalogue of compliant relevant services and tools.

At the core of the BKH is the FAIR Data Place (FDP), where users can familiarise themselves with each of the participating biodiversity infrastructures and network organisations, and also learn about the specific services they provide. There, anyone can explore various biodiversity data tools and services by browsing by their main data type, e.g. specimens, sequences, taxon names, literature.

While the project might be coming to an end, she pointed out, the BKH is here to stay as a navigation system in a universe of interconnected biodiversity research infrastructures.

To do this, not only will the partners continue to maintain it, but it will also remain open to any research infrastructure that wishes to feature its own tools and services compliant with the linked and FAIR data requirements set by the BiCIKL consortium.

On the event’s website you can access the BiCIKL’s slides presentation as presented at the EBR III conference.

What else was on at the EBR III?

Indisputably, the ‘hot’ topics at the EBR III were the novel technologies for remote and non-invasive, yet efficient biomonitoring; the utilisation of data and other input sourced by citizen scientists; as well as leveraging different types and sources of biodiversity data, in order to better inform decision-makers, but also future-proof the scientific knowledge we have collected and generated to date.

Project’s coordinator Dr Quentin Groom presents the B-Cubed’s approach towards standardised access to biodiversity data for the use of policy-making at the EBR III conference.

Amongst the other Horizon Europe projects presented at the EBR III conference was B-Cubed (Biodiversity Building Blocks for policy). On Monday, the project’s coordinator Dr Quentin Groom (Meise Botanic Garden) familiarised the conference participants with the project, which aims to standardise access to biodiversity data, in order to empower policymakers to proactively address the impacts of biodiversity change.

You can find more about B-Cubed and Pensoft’s role in it in this blog post.

On the event’s website you can access the B-Cubed’s slides presentation as presented at the EBR III conference.

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Dr France Gerard (UK Centre for Ecology & Hydrology) talks about the challenges in using raw data – including those provided by drones – to derive habitat condition metrics.

MAMBO: another Horizon Europe project where Pensoft has been contributing with expertise in science communication, dissemination and exploitation, was also an active participant at the event. An acronym for Modern Approaches to the Monitoring of BiOdiversity, MAMBO had its own session on Tuesday morning, where Dr Vincent Kalkman (Naturalis Biodiversity Center), Dr France Gerard (UK Centre for Ecology & Hydrology) and Prof. Toke Høye (Aarhus University) each took to the stage to demonstrate how modern technology developed within the project is to improve biodiversity and habitat monitoring. Learn more about MAMBO and Pensoft’s involvement in this blog post.

MAMBO’s project coordinator Prof. Toke T. Høye talked about smarter technologies for biodiversity monitoring, including camera traps able to count insects at a particular site.

On the event’s website you can access the MAMBO’s slides presentations by Kalkman, Gerard and Høye, as presented at the EBR III conference.

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The EBR III conference also saw a presentation – albeit remote – from Prof. Dr. Florian Leese (Dean at the University of Duisburg-Essen, Germany, and Editor-in-Chief at the Metabarcoding and Metagenomics journal), where he talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. 

Amongst the key tasks here, he pointed out, are the alignment of DNA-based methods with the Global Biodiversity Framework; central push and funding for standards and guidance; publication of data in portals that adhere to the best data practices and rules; and the mobilisation of existing resources such as the meteorological ones. 

Prof. Dr. Florian Leese talked about the promise, but also the challenges for DNA-based methods to empower biodiversity monitoring. He also referred to the 2022 Forum Paper: “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al.

He also made a reference to the Forum Paper “Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms” by R. Henrik Nilsson et al., where the international team provided a brief rationale and an overview of guidelines targeting the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. In the study, published in the Metabarcoding and Metagenomics journal in 2022, they also introduced a living version of these guidelines, which continues to encourage feedback and interaction as new techniques and best practices emerge.

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You can find the programme on the conference website and see highlights on the conference hashtag: #EBR2024.

Don’t forget to also explore the Biodiversity Knowledge Hub for yourself at: https://biodiversityknowledgehub.eu/ 

“Tiny, beautiful, and completely unknown animals”: Citizen scientists discover new beetles from the Borneo forest

The field trip allowed laypeople to participate in the study of biodiversity, and to discover and name a new species.

The undiscovered small beetles in the tropical rainforest are probably endless. But that did not discourage citizen scientists on expeditions to the Ulu Temburong forest in Borneo to keep adding them to scientific records, one at a time. Together with a team of researchers, they published a new species, Clavicornaltica mataikanensis in the open-access peer-reviewed Biodiversity Data Journal.

Clavicornaltica mataikanensis. Credit: Taxon Expeditions – Holm Friedrich

The minute, two-mm-long leaf beetle that lives on the forest floor is the latest discovery of Taxon Expeditions, which organises scientific field trips for teams consisting of both scientists and lay people. Unlike other science/adventure trips, Taxon Expeditions organises real scientific expeditions for lay people, guiding them in the discovery of new species of animals, by focusing on the thousands of ‘little things that run the world’.

Citizen scientists, students, and researchers working together in the rainforest. Credit: Taxon Expeditions – Sotiris Kountouras

Clavicornaltica mataikanensis, named for the stream Mata Ikan (“fish eye”) that runs in the valley where it was found, is one of a plethora of tiny beetle species that live in the leaf litter of tropical forests—and most of them have not yet been scientifically described and named. At 2 mm long, the flea beetle is actually one of the largest among its relatives – which might explain why so little is known about their ecology and diversity.

The Ulu Temburong forest in Brunei. Credit: Taxon Expeditions – Sotiris Kountouras

The field trip, in which local students and researchers also took part, gave untrained lay people the opportunity to participate in the study of this hidden world of biodiversity and in the process of naming and publishing new species. Participant Lehman Ellis, from the US, says it was “exciting and beautiful” to be part of the discovery.

Citizen scientist Eleonora Nigro in the field lab working on the publication. Credit: Taxon Expeditions – Iva Njunjić

Entomologist and founder of Taxon Expeditions, Dr. Iva Njunjić, says: “We introduce the general public to all these tiny, beautiful, and completely unknown animals, and show them that there is a whole world still to be discovered.”

Research article:

Otani S, Bertoli L, Lucchini F, van den Beuken TPG, Boin D, Ellis L, Friedrich H, Jacquot B, Kountouras S, Lim SR, Nigro E, Su’eif S’ie, Tan WH, Grafe U, Cicuzza D, Delledonne M, Njunjić I, Schilthuizen M (2024) A new, unusually large, Clavicornaltica Scherer, 1974 flea beetle from Borneo, described and sequenced in the field by citizen scientists (Coleoptera, Chrysomelidae, Galerucinae). Biodiversity Data Journal 12: e119481. https://doi.org/10.3897/BDJ.12.e119481

BiCIKL project sums up outcomes and future prospects at a Final GA in Cambridge

On multiple occasions, the participants agreed that the Biodiversity Knowledge Hub must be the flagship outcome of BiCIKL. 

The city of Cambridge and the Wellcome Campus hosted the Final General Assembly of the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library): a 36-month endeavour that saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. Consortium members who could not attend the meeting in Cambridge joined the meeting remotely.

The 3-day meeting was organised by local hosts European Molecular Biology Laboratory (EMBL) and ELIXIR in collaboration with Pensoft Publishers.

After a welcome cocktail reception on Monday evening at Hilton Cambridge City Centre, on Tuesday, the consortium made an early start with a recap of BiCIKL’s key milestones and outputs from the last three years. All Work Package leaders had their own timeslot to discuss the results of their collaborations.  

They all agreed that the Biodiversity Knowledge Hub – the one-stop portal for understanding the complex – yet increasingly interconnected landscape of biodiversity research infrastructures – is likely the flagship outcome of BiCIKL. 

Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers at the BiCIKL’s third and final General Assembly in Cambridge, United Kingdom.

In the afternoon, the participants focused on the services developed under BiCIKL. Amongst the many services resulting from the project some were not originally planned. Rather those were the ‘natural’ products of the dialogue and collaboration that flourished within the consortium throughout the project. “A symptom of passion,” said Prof. Lyubomir Penev, project coordinator of BiCIKL and founder/CEO of Pensoft Publishers.

An excellent example of one such service is what the partners call the “Biodiversity PMC”, which brings together biodiversity literature from thousands of scholarly journals and over 500,000 taxonomic treatments, in addition to the biomedical content available from NIH’s PubMed Central, into the SIB Literature Services (SIBiLS) database. What’s more, users at SIBiLS – be it human or AI – can now use advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions. Read more about the “Biodiversity PMC” in its recent official announcement.

Far from being the only one, the “Biodiversity PMC” is in good company: from the blockchain-based technology of LifeBlock to the curation of the DNA sequences by PlutoF, the BiCIKL project consortium takes pride in having developed twelve services dedicated to FAIR and linked ready-to-use biodiversity data. 

All those services are already listed in the FAIR Data Place within the Biodiversity Knowledge Hub, where each is presented with its own video. For many services, from the same page, visitors can also download factsheets meant to serve as user guidelines. All will also be featured in the EOSC catalogue.

All services developed under BiCIKL with links to their explanatory videos:

On Wednesday, the consortium focused on BiCIKL’s activities from the Transnational and Virtual Access Pillar, which included both presentations by each open call leader and VA leader, as well as open discussions and a recap of what the teams have learnt from these experiences. 

A panel discussion took place on Thursday as part of an open event, where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus.

Thursday was dedicated to an open event where BiCIKL partners and ELIXIR Biodiversity and Plant Communities came together to discuss the Future of Biodiversity and Genomics data integration at the EMBL Wellcome Genome Campus. You can find the agenda on BiCIKL’s website.

After 36 months of action, the BiCIKL project will officially end in April 2024, but does it mean that all will be done and dusted come May 2024? Certainly not, point out the partners. 

To ensure that the Biodiversity Knowledge Hub will not only continue to exist but will not cease to grow in both use and participation, the one-stop portal will remain under the maintenance of LifeWatch ERIC. 

In conclusion, we could say that an appropriate payoff for the project is “Stick together!” as put by BiCIKL’s Joint Research Activity Leader Dr. Quentin Groom.

Final words at the third and last General Assembly of the BiCIKL project.

You can find highlights from the BiCIKL General Assembly meeting on X via the #BiCIKL_H2020 hashtag (in association with #Cambridge and #finalGA)

BiCIKL keeps on adding project outcomes in own collection in RIO Journal
All research outputs, including the approved grant proposal, policy briefs, guidelines papers and research articles associated with the project, remain openly accessible from the BiCIKL project outcomes collection in RIO Journal: https://doi.org/10.3897/rio.coll.105.

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All BiCIKL project partners:

Towards the “Biodiversity PMC”: a literature database supporting advanced content queries

The indexing is one of the major outcomes from the partnerships within the Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL)

Amongst the major outcomes from the currently nearly completed Horizon 2020-funded project Biodiversity Community Integrated Knowledge Library (BiCIKL) – dedicated to making biodiversity data FAIR and bi-directionally linked – brings the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

In a joint effort between the Swiss-based Text Mining group of Patrick Ruch at SIB (developing SIBiLS), the text- and data-mining association Plazi and scientific publisher Pensoft, the long-time collaborators have started feeding full-text content of over 500,000 taxonomic treatments extracted by Plazi and tens of thousands full-text articles from 40 well-renowned biodiversity journals published by Pensoft to the SIBiLS database. 

What this means is that users at SIBiLS – be it human or AI – have now gained access to advanced text- and data-mining tools, including AI-powered factoid question-answering capacities, to query all this full-text indexed content and seek out, for example, species traits and biotic interactions.

To index and directly feed the content from its 40+ academic outlets at SIBiLS, Pensoft relies on advanced and full-text TaxPub JATS XML journal publication workflow, powered by the ARPHA publishing platform. Meanwhile, Plazi uses its GoldenGate text- and data-mining software to harvest taxon treatments from over 80 journals stored at TreatmentBank and the Biodiversity Literature Repository, and then further re-used by GBIF, OpenBiodiv and now by SiBILS.

Seen as a pilot, the indexing – the partners believe – could soon be extended with other journals relying on modern publishing or converted legacy publications. 

In fact, ever since its launch in 2020, the queryable database SIBiLS has been retrieving relevant full-text papers directly from the NIH’s PubMed Central, including Pensoft’s ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal and Comparative Cytogenetics. 

However, there were still gaps left to bridge before SIBiLS could indeed be dubbed “the Biodiversity PMC”, and those have mostly been about volume and breadth of content. While the above-mentioned five journals by Pensoft had long been indexed by SIBiLS through harvesting PMC, those had been quite an exception since, several years ago, a reorganisation at PMC moved the focus of the database to almost exclusively biomedical content, thus leaving biodiversity journals out of the scope of the database.

In the meantime, while Plazi has been feeding SIBiLS a growing volume of taxonomic treatments and visual data, as it was exponentially increasing the number of publishers and journals it mined data from, a lot of biodiversity data (e.g. genetic, molecular, ecological) published in the article narratives that were not taxon treatments could not make it to the portal.

“We all know the advantages and practical uses PMC offers to its users, so we cannot miss the opportunity to incorporate this well-proven approach to navigate the data deluge in biodiversity science. Undoubtedly, it is an extremely ambitious and demanding task. Yet, I believe that, at the BiCIKL consortium, we have made it pretty clear we have the necessary expertise, know-how and aspiration to take on the challenge,”

said Prof. Lyubomir Penev, founder/CEO at Pensoft and project coordinator of BiCIKL.

“For far too long, scientific knowledge about biodiversity has been imprisoned in a continuously growing corpus of scientific outputs, which – most of the time – are published in unstructured formats, such as PDF, or as paywalled content, and often locked by both! This means that they are – at best – difficult to access and comprehend by computer algorithms. In the meantime, we need all that knowledge, in order to accelerate our understanding of the dynamics of the global biodiversity crisis and to efficiently assess the impact of climate change. This is why the need for advanced workflows and tools to annotate, mine, query and discover new facts from the available literature is more than obvious,”

added Dr. Donat Agosti, President at Plazi.

“In the course of the BiCIKL project, at SIBiLS, we started indexing a larger set of biodiversity-related contents in the broad sense, including environmental sciences and ecology, to build a new literature database, or what we now call ‘Biodiversity PMC’. Now, with the help of Plazi and Pensoft, we provide a unique entry point to half a million taxonomic treatments, which were not included into the original PubMed Central. Next on the list is to expand our network of literature sources and continue this exponential growth of queryable biodiversity knowledge to turn Biodiversity PMC into the “One Health” library. We promise to keep you posted,”

said Dr. Patrick Ruch, Group Leader at SIB and Head of Research at HES-SO, HEG Geneva, Switzerland. 

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Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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About the SIB Swiss Institute of Bioinformatics:

SIB is an internationally recognized non-profit organisation, dedicated to biological and biomedical data science. SIB’s data scientists are passionate about creating knowledge and solving complex questions in many fields, from biodiversity and evolution to medicine. They provide essential databases and software platforms as well as bioinformatics expertise and services to academic, clinical, and industry groups. With the recent creation of the Environmental Bioinformatics group, led by Robert Waterhouse, SIB is engaged in an unprecedented effort to streamline data across molecular biology, health and biodiversity. SIB also federates the Swiss bioinformatics community of some 900 scientists, encouraging collaboration and knowledge sharing.

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About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; is co-founder of the Biodiversity Literature Repository at Zenodo, participates in the development of new models for publishing taxonomic treatments in order to maximise interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data. Plazi is a major contributor to the Global Biodiversity Information Facility.