In a world increasingly defined by data-driven decisions, biodiversity research stands to benefit from standardized and accessible data. Despite their importance for research, biodiversity datasets often fail to meet FAIR (Findable, Accessible, Interoperable, Reusable) standards, leading to concerns about data quality, reliability, and accessibility.
To address this, we propose a framework to retrieve, refine and align secondary biodiversity data with FAIR standards, utilizing the Darwin Core model. We followed four steps:
data localization (systematic review)
quality validation
standardization using the Darwin Core standard
sharing and archive in the appropriate repository.
Our approach integrates data validation and quality control steps to ensure that secondary data sets can be trusted.
Our study in Biodiversity Data Journalfocused on ecotonal estuarine ecosystems near the easternmost Amazon, where we recovered data from 46,000 individuals representing 3,871 taxa across eight biotic groups (birds, amphibians, reptiles, mammals, fish, phytoplankton, benthos, and plants) from 1985 to 2022. These data were used to illustrate how our strategy improves validation, making the data more reliable for macroecological modeling and conservation management. As data becomes more standardized, researchers around the world will be better equipped to collaborate, identify trends, protect ecosystems, and advance sustainability efforts.
Relationships between numbers of taxa and occurrences gathered through an extensive review of secondary biodiversity data from the Golfão Maranhense area, in the estuarine regions of eastern Amazonia.
Accessible biodiversity data empowers stakeholders and provides critical insights into ecosystem health and species conservation. However, without standardized formats, this data is often fragmented, incomplete, or difficult to compare. By creating a consistent framework for collecting, storing, and sharing data, we are opening the door to more informed decision-making and innovation in biodiversity conservation.
The key to conserving biodiversity is collaboration and transparency. By prioritizing accessible and standardized data, we ensure that vital information reaches those who need it most – whether it’s for scientific study, habitat management or policymaking.
Let’s continue to make biodiversity data a tool for global change!
Research article:
Marques N, Soares CDdeM, Casali DdeM, Guimarães E, Fava F, Abreu JMdaS, Moras L, Silva LGda, Matias R, Assis RLde, Fraga R, Almeida S, Lopes V, Oliveira V, Missagia R, Carvalho E, Carneiro N, Alves R, Souza-Filho P, Oliveira G, Miranda M, Tavares VdaC (2024) Retrieving biodiversity data from multiple sources: making secondary data standardised and accessible. Biodiversity Data Journal 12: e133775. https://doi.org/10.3897/BDJ.12.e133775
Pensoft joins the newly funded Biodiversa+ project ANTENNA focused on making technology work for monitoring pollinators and is tasked with the communication, dissemination and exploitation activities.
The overarching goal of ANTENNA is to fill key monitoring gaps through advancing innovative technologies that will underpin and complement EU-wide pollinator monitoring schemes, and to provide tested transnational pipelines from monitoring activities to curated datasets and enhanced indicators that support pollinator-relevant policyand end-users.
The ANTENNA project answers the BiodivMon call, which was launched in September 2022 by Biodiversa+ in collaboration with the European Commission. The BiodivMon call sought proposals for three-year research projects to improve transnational monitoring of biodiversity and ecosystem change, emphasising innovation and harmonisation of biodiversity datacollection and management methodologies, addressing knowledge gaps on biodiversity status and trends to combat biodiversity loss, and the effective use of existing biodiversity monitoring data.
Supporting the work of Work Package #5: “Project coordination, and communication”, Pensoft is dedicated to maximising the project’s impact by employing a mix of channels to inform stakeholders about the results from ANTENNA and raise public awareness about pollinators.
Pensoft is also tasked with creating and maintaining a clear and recognisable project brand, promotional materials, website, social network profiles, internal communication platform, and online libraries. Another key responsibility is the development, implementation and regular updates of the project’s communication, dissemination and exploitation plans, that ANTENNA is set to follow for the next four years.
On 14-15 March 2024, ANTENNA held its official kick off meeting. Project partners came together in Halle, Germany for two days to outline objectives, discuss strategies, and set the groundwork for this venture.
Specifically, the combined expertise of the consortium will address the following objectives:
Advanceautomated sample sorting and image recognition tools from individual prototypesto systems that can be adopted by practitioners
Expand pollinator monitoring to under-researched pollinator taxa, ecosystems, and pressures
Quantify the added value of novel monitoring systems in comparison and combination with ‘traditional’ methods in terms of cost effectiveness
Provide a framework for integrative monitoring by combining multiple data streams and. The framework will also support the development of near real-time forecasting models as bases for early warning systems;
Upscale local demonstrations into the implementation of large-scale transnational pipelines and provide context-specific guidance to the use of policy-makers and other users who might need to select monitoring methods and indicators.
*Pensoft Publishers is a subcontractor tasked by the UFZ with multiple communication, dissemination and exploitation activities as part of Work Package 5.
The beetle species Grebennikovius basilewskyi. Numbers next to arrows indicate patterns of phenotype statements explained in the section “Phenoscript: main patterns of phenotype statements”. Arrow numbers from T1 to T5 illustrate individual body parts. See more in the research study.
One of the most beautiful aspects of Nature is the endless variety of shapes, colours and behaviours exhibited by organisms. These traits help organisms survive and find mates, like how a male peacock’s colourful tail attracts females or his wings allow him to fly away from danger. Understanding traits is crucial for biologists, who study them to learn how organisms evolve and adapt to different environments.
To do this, scientists first need to describe these traits in words, like saying a peacock’s tail is “vibrant, iridescent, and ornate”. This approach works for small studies, but when looking at hundreds or even millions of different animals or plants, it’s impossible for the human brain to keep track of everything.
Computers could help, but not even the latest AI technology is able to grasp human language to the extent needed by biologists. This hampers research significantly because, although scientists can handle large volumes of DNA data, linking this information to physical traits is still very difficult.
To solve this problem, researchers from the Finnish Museum of Natural History, Giulio Montanaro and Sergei Tarasov, along with collaborators, have created a special language called Phenoscript. This language is designed to describe traits in a way that both humans and computers can understand. Describing traits with Phenoscript is like programming a computer code for how an organism looks.
Phenoscript uses something called semantic technology, which helps computers understand the meaning behind words, much like how modern search engines know the difference between the fruit “apple” and the tech company “Apple” based on the context of your search.
“This language is still being tested, but it shows a lot of promise. As more scientists start using Phenoscript, it will revolutionise biology by making vast amounts of trait data available for large-scale studies, boosting the emerging field of phenomics,”
explains Montanaro.
In their research article, newly published in the open-access, peer-reviewed Biodiversity Data Journal, the researchers make use of the new language for the first time, as they create semantic phenotypes for four species of dung beetles from the genus Grebennikovius. Then, to demonstrate the power of the semantic approach, they apply simple semantic queries to the generated phenotypic descriptions.
Finally, the team takes a look yet further ahead into modernising the way scientists work with species information. Their next aim is to integrate semantic species descriptions with the concept of nanopublications, “which encapsulates discrete pieces of information into a comprehensive knowledge graph”. As a result, data that has become part of this graph can be queried directly, thereby ensuring that it remains Findable, Accessible, Interoperable and Reusable (FAIR) through a variety of semantic resources.
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Research paper:
Montanaro G, Balhoff JP, Girón JC, Söderholm M, Tarasov S (2024) Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae). Biodiversity Data Journal 12: e121562. https://doi.org/10.3897/BDJ.12.e121562
What expert recommendations did the BiCIKL consortium give to policy makers and research funders to ensure that biodiversity data is FAIR, linked, open and, indeed, future-proof? Find out in the blog post summarising key lessons learnt from the Horizon 2020 project.
Within theBiodiversity 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.
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.
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.
“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,”
“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,”
“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,”
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.
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.
‘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.
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.
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
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.
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.
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, GerardandHøye, 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.
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.
Dikow, an esteemed entomologist specialising in Diptera and cybertaxonomy, is the new Editor-in-Chief of the leading scholarly journal in systematic zoology and biodiversity
Esteemed entomologist specialising in true flies (order Diptera) and cybertaxonomy, Dr Torsten Dikow was appointed as the new Editor-in-Chief of the leading open-access peer-reviewed journal in systematic zoology and biodiversity ZooKeys.
Today, Dikow is a Research Entomologist and Curator of Diptera and Aquatic Insects at the Smithsonian National Museum of Natural History (Washington, DC, USA), where his research interests encompass the diversity and evolutionary history of the superfamily Asiloidea – or asiloid flies – comprising curious insect groups, such as the assassin flies / robber flies and the mydas flies. Amongst an extensive list of research publications, Dikow’s studies on the diversity, biology, distribution and systematics of asiloid flies include the description of 60 species of assassin flies alone, and the redescription of even more through comprehensive taxonomic revisions.
During his years as a postdoc at the Field Museum (Illinois, USA), Dikow was earnestly involved in the broader activities of the Encyclopedia of Life through its Biodiversity Synthesis Center (BioSynC) and the Biodiversity Heritage Library (BHL). There, he would personally establish contacts with smaller natural history museums and scientific societies, and encourage them to grant digitisation permissions to the BHL for in-copyright scientific publications. Dikow is a champion of cybertaxonomic tools and making biodiversity data accessible from both natural history collections and publications. He has been named a Biodiversity Open Data Ambassador by the Global Biodiversity Information Facility (GBIF).
Dikow is no stranger to ZooKeys and other journals published by the open-access scientific publisher and technology provider Pensoft. For the past 10 years, he has been amongst the most active editors and a regular author and reviewer at ZooKeys, Biodiversity Data Journal and African Invertebrates.
“Publishing taxonomic revisions and species descriptions in an open-access, innovative journal to make data digitally accessible is one way we taxonomists can and need to add to the biodiversity knowledge base. ZooKeys has been a journal in support of this goal since day one. I am excited to lend my expertise and enthusiasm to further this goal and continue the development to publish foundational biodiversity research, species discoveries, and much more in the zoological field,”
ZooKeys is a peer-reviewed, open-access, rapidly disseminated journal launched to accelerate research and free information exchange in taxonomy, phylogeny, biogeography and evolution of animals. ZooKeys aims to apply the latest trends and methodologies in publishing and preservation of digital materials to meet the highest possible standards of the cybertaxonomy era.
ZooKeys publishes papers in systematic zoology containing taxonomic/faunistic data on any taxon of any geological age from any part of the world with no limit to manuscript size. To respond to the current trends in linking biodiversity information and synthesising the knowledge through technology advancements, ZooKeys also publishes papers across other taxon-based disciplines, such as ecology, molecular biology, genomics, evolutionary biology, palaeontology, behavioural science, bioinformatics, etc.
Imagine having access to all the two billion biological collections of the world from your desktop! Not only to browse, but to search with artificial intelligence. We recently published a paper where we envisage what might be possible, such as searching all specimen labels for a person’s signature, studying the patterns of butterflies’ wings, or reconstructing a historic expedition.
Numbers of digital images from biodiversity collections are increasing exponentially. Herbariums have led the way with tens of millions of images available, but images of pinned insects will soon overtake plants.
Numbers of accessible images of specimens are increasing exponentially. Plants lead the way, but insects are increasing at the fastest rate. This graph was created from snapshots of the Global Biodiversity Information Facility and is undoubtedly an underestimate of the actual number of specimens for which images exist. See how this was created in Groom et al. (2023).
At one time, if you wanted access to biological collections, you had to travel. Now we are used to visiting collections online, where we can view images of specimens and their details on our desktops. Nevertheless, biological collection images are still dispersed and this limits their effective use, not just for people, but also for computers. One of the promises of making specimens digital is being able to apply machine learning to these images. Yet the real benefits of machine access to specimens can only be realised through massive access to collection images and the ability to apply these techniques to hundreds of collections and millions of specimens.
Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude.
In our paper in Biodiversity Data Journal, we examined some of the numerous uses for machine learning in digital collections. These include an enormous potential to extract traits of organisms, from the size and shape of different organs, to their colours, patterns, and phenology. Imagine examining collections globally for the variation and evolution of wing coloration in butterflies, or studying the size and shape of leaves in research that transverses habitats and gradients of latitude and altitude. We would not only be able to study the intricacies of evolution, but also practical subjects, such as the mechanics of pollination in insects, adaptations to drought in plants, and adaptations to weediness in invasive species.
Machine access to these images will also provide an unparalleled view of the history of the biological sciences, the specimens used to describe species, the evidence for evolution, the people involved and institutions that contributed. Such transparency may reveal some amazing stories of scientific exploration, but will undoubtedly also shed light on some of the less exemplary actions of colonialism. Yet if we are to redress the injustices of the past we need to have a balanced view of collections, and we should do this openly.
Specimen labels provide numerous clues to their history often in the form of stamps and emblems. ABR0000013433048 Meise Botanic Garden (CC-BY-SA 4.0). B USCH0030719, A.C. Moore Herbarium at the University of South Carolina (public domain). CE00809288, Royal Botanic Garden Edinburgh (public domain). D USCH0030719, University of South Carolina (public domain). EE00919066, Royal Botanic Garden Edinburgh (public domain). FBR0000017682725, Meise Botanic Garden (CC-BY-SA 4.0). GP00605317, Museum National d’Histoire Naturelle, Paris (CC-BY 4.0). H LISC036829, Instituto de Investigação Científica Tropical (CC-BY-NC 4.0). l PC0702930, Muséum National d’Histoire Naturelle, Paris (CC-By 4.0). J same specimen as (B). K PC0702930 Muséum National d’Histoire Naturelle, Paris (CC-BY 4.0). L101178648, Missouri Botanical Garden (CC-BY-SA 4.0).
With such unparalleled access to collections, we could travel vicariously to times and places that are hard to reach in any other way. Fieldwork is expensive and time-consuming, and can’t provide the historic perspective of collections, let alone the geographic extent. Furthermore, digital resources have the potential to democratise collections, allowing anyone the opportunity to study these collections irrespective of location.
Is such a vision of integrated digital collections possible? It certainly is! The technologies already exist, not just for machine learning, but also to create the infrastructure to provide access to millions of digital images and their metadata. Initiatives, such as DiSSCo in Europe and iDigBio in the USA are moving in this direction. Yet, we conclude that the main challenge to realising this vision of the future is a sociopolitical one. Can so many institutions and funders work together to pool their resources? Can collections in rich countries share the sovereignty of their collections with the countries where many of the specimens originated?
If you too share the dream, we encourage you to support or contribute to initiatives working in this direction, whether through funding, collaboration, or sharing knowledge. If the full potential of digital collections is to be realised, we need to think big and work together.
Research article:
Groom Q, Dillen M, Addink W, Ariño AHH, Bölling C, Bonnet P, Cecchi L, Ellwood ER, Figueira R, Gagnier P-Y, Grace OM, Güntsch A, Hardy H, Huybrechts P, Hyam R, Joly AAJ, Kommineni VK, Larridon I, Livermore L, Lopes RJ, Meeus S, Miller JA, Milleville K, Panda R, Pignal M, Poelen J, Ristevski B, Robertson T, Rufino AC, Santos J, Schermer M, Scott B, Seltmann KC, Teixeira H, Trekels M, Gaikwad J (2023) Envisaging a global infrastructure to exploit the potential of digitised collections. Biodiversity Data Journal 11: e109439. https://doi.org/10.3897/BDJ.11.e109439
The database is a groundbreaking and pioneering initiative set to revolutionise our understanding of the rich biodiversity of Mindanao, the second-largest island group in the Philippines.
The Philippine Archipelago, with more than 7,100 islands, has one of the highest levels of endemism globally and is a hotspot for biodiversity conservation. Mindanao, the second largest group of islands in the country, is a treasure trove of terrestrial species, boasting one of the highest densities of unique flora and fauna on the planet. However, despite its ecological significance, comprehensive biodiversity records and data for the region have remained inaccessible until now.
The Mindanao Open Biodiversity Information (MOBIOS+) database aims to bridge these critical data gaps by compiling biodiversity information from the 21st century. This monumental undertaking seeks to enhance our understanding of Mindanao’s biodiversity trends, while establishing a database that is openly accessible to researchers and conservationists worldwide.
MOBIOS+ is the first of its kind and, currently, the most comprehensive attempt to create a consolidated database for the biodiversity of Mindanao based on publicly available literature. With a vast collection of biodiversity data, this database will be an invaluable resource to advance regional biodiversity research and analysis.
“It will further facilitate the identification of species and areas that require immediate conservation prioritisation and action, addressing the urgent challenges posed by our rapidly changing planet,” the researchers behind the project write in their data paper, published in the open-access, peer-reviewed Biodiversity Data Journal.
Team members of the MOBIOS+ consortium curating the dataset.
The MOBIOS+ database, available through the Global Biodiversity Information Facility (GBIF) platform, currently comprises an impressive 12,813 georeferenced specimen occurrences representing 1,907 unique taxa. These span across ten animal classes inhabiting terrestrial and freshwater environments within the Mindanao faunal region. The project aims to continuously update the species database, complementing on-ground biodiversity efforts in Mindanao.
Diversity and distribution of species occurrence records across taxonomic groups included in the first version of the MOBIOS+ database. The diversity of species (percentage, %) according to class compared to the overall number of species recorded in the MOBIOS+ database (a); and the total number of species and the number of georeferenced occurrences per animal class (b).
Associate Professor Krizler Tanalgo of the Ecology and Conservation Research Laboratory at the University of Southern Mindanao, the project leader behind MOBIOS+, shared his thoughts on this initiative, saying:
“We aim to democratise biodiversity information, making it readily available to researchers, policymakers, and conservation biologists. By doing so, we hope to facilitate well-informed decisions to address pressing environmental challenges, with a particular focus on the often underrepresented Mindanao region, which tends to receive limited attention in terms of research and funding.”
Distribution of biodiversity records across taxonomic groups from published papers.
“The MOBIOS+ database is not only a testament to the dedication of the scientific community, but also a beacon of hope for the future of biodiversity conservation in Mindanao and beyond. It will support researchers and conservationists in identifying species and areas that require immediate prioritisation and action, safeguarding the unique and fragile ecosystems of this extraordinary region.”
The Biodiversity Community Integrated Knowledge Library (BiCIKL) project, funded by the European Union Horizon 2020 Research and Innovation Action under grant agreement No 101007492, has supported the publication of this work. The work is part of a special collection supported by the project and looking to demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
Research article: Tanalgo KC, Dela Cruz KC, Agduma AR, Respicio JMV, Abdullah SS, Alvaro-Ele RJ, Hilario-Husain BA, Manampan-Rubio M, Murray SA, Casim LF, Pantog AMM, Balase SMP, Abdulkasan RMA, Aguirre CAS, Banto NL, Broncate SMM, Dimacaling AD, Fabrero GVN, Lidasan AK, Lingcob AA, Millondaga AM, Panilla KFL, Sinadjan CQM, Unte ND (2023) The MOBIOS+: A FAIR (Findable, Accessible, Interoperable and Reusable) database for Mindanao’s terrestrial biodiversity. Biodiversity Data Journal 11: e110016. https://doi.org/10.3897/BDJ.11.e110016
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You can find all contributions published in the “Linking FAIR biodiversity data through publications: The BiCIKL approach” article collection in the open-access, peer-reviewed Biodiversity Data Journal on: https://doi.org/10.3897/bdj.coll.209.
