Herbaria – collections of preserved plant specimens – are crucial in botanical research and biodiversity conservation. Digitising these collections is an important step towards making data available to all, preserving specimens by reducing the need for handling, and creating new research opportunities.
Mass digitisation of herbarium specimens on a conveyor belt at Meise Botanic Garden, allowing the imaging of 3,000–5,000 specimens per day.
Meise Botanic Garden recently completed a six-year project to digitise approximately three million specimens of their herbarium collection. While it was a big change for their organisation, it was one they deemed necessary to bring their collection into the digital age.
Joint restoration session of the herbarium team at Meise Botanic Garden.
Based on their experience, the team published ten valuable lessons they learned during the process to assist other institutions embarking on similar digitisation projects. These lessons are available in the open-access journal PhytoKeys.
1. Knowing yourself is the beginning of all wisdom ― Aristotle
Before starting digitisation, it is important to understand the full scope of your collection. This involves detailed inventory checks and assessments of the state of the specimens. Knowing the exact number and condition of the specimens will help in accurate budgeting and planning. A detailed inventory of a representative tenth of your collection can be extrapolated to the entire collection.
2. Prioritise (if lack of money forces you to do so)
If resources are limited, prioritising which parts of the collection to digitise first is key. Consider factors such as the scientific importance of the specimens, their physical state, and stakeholder needs. It is important to note that digitising the entire collection can be more efficient than selecting subcollections, as partial digitisation can complicate management.
3. Learn from other people’s successes – and mistakes
Do not reinvent the wheel. Engage with other institutions that have undertaken similar projects to learn from their successes and mistakes. Follow existing guidelines and adapt them to fit your specific needs. If you think you have a better way of doing things, talk it over with someone with experience.
4. Decide whether to do it yourself or have it done for you
Deciding whether to conduct the digitisation in-house or to outsource it depends on available resources. Consider the skills and availability of your staff and the costs associated with outsourcing. Some tasks, such as imaging or data transcription, might be more efficiently handled by external specialists.
5. Make a plan
A well-thought-out plan is crucial. Define workflows, procedures, and quality control mechanisms. And be specific about your requirements when outsourcing parts of the project to avoid any misunderstandings.
6. Go shopping
Ensure that all necessary supplies, such as barcodes, storage containers, and IT infrastructure, are in place before starting the digitisation process. Bulk purchasing is often cost-effective, and having everything ready will prevent delays.
7. Make your collection look its best for the photographer
Prepare the specimens for imaging by incorporating pre-digitisation curation steps like repairing damaged specimens and adding barcodes.
8. Expect problems, particularly ones that you don’t expect
Problems will arise, from equipment malfunctions to human errors. Establish quality control processes to catch issues early. Automate checks where possible and ensure prompt human review for aspects like image focus and lighting.
9. Make your data visible – make a big deal of it
Making digitised data publicly accessible is vital. Use online portals and ensure the data adheres to FAIR principles (Findable, Accessible, Interoperable, Reusable). Publicity will increase the use and impact of your collection.
10. Save your data for the future
Make sure the digitised data is backed up in a secure, offsite archive. Long-term storage solutions should be considered to preserve the data for future use. And factor this ongoing cost into the budget.
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To read extended advice from Meise Botanic Garden, as well as four case studies, check out the full research paper below:
Original source
De Smedt S, Bogaerts A, De Meeter N, Dillen M, Engledow H, Van Wambeke P, Leliaert F, Groom Q (2024) Ten lessons learned from the mass digitisation of a herbarium collection. PhytoKeys 244: 23-37. https://doi.org/10.3897/phytokeys.244.120112
Late May 2024 saw the whole content ever published in VCS added to the Core Collection of the renowned academic platform, further boosting its discoverability, accessibility and reliability to researchers and other stakeholders alike, confirms the Indexing team of Pensoft and the ARPHA scholarly publishing platform.
“Many thanks to IAVS as owner and Pensoft as publisher, who made this success story possible. However, most of all, this early inclusion into the Web of Science Core Edition is due to the good articles of our authors and the great volunteer service our Associate Editors, Guest Editors, Linguistic Editors, Editorial Review Board members, and other reviewers did and do for VCS,”
the Chief Editors comment on the latest success.
The news means that VCS is soon to receive its very first Journal Impact Factor (JIF): allegedly the most popular and sought after journal-level metric, which annually releases the citation (or “impact”) rate of a given scholarly journal over the last period. By the end of next month, for example, we will know how different journals indexed by WoS have performed compared to each other, based on the number of citations received in 2023 (from other journals indexed by WoS) for papers published in 2021 and 2022 combined.
In 2022, VCS and its all-time publications were also featured by the largest and similarly acclaimed scientific database: Scopus, thus receiving its very first Scopus CiteScore* last June. At 2.0, the result instantly gave a promise of the widely appreciated content published in the journal.
In an editorial, published in the beginning of 2024, the Chief Editors assessed the performance of the journal and analysed the available data from Scopus to predict the citation rates for the journal in the next few years. There, the team also compared the journal’s latest performance with similar journals, including the other two journals owned by the IAVS (i.e. Applied Vegetation Science and Journal of Vegetation Science). Given that as of May 2024 the Scopus CiteScoreTracker for VCS reads 2.5, their optimistic forecasts seem rather realistic.
“The VCS articles of 2023 were on average even better cited than those in Applied Vegetation Science of the same year and had reached about the same level as Journal of Vegetation Science and Biodiversity and Conservation,”
they concluded.
In a recent post, published on the IAVS blog, on behalf of the four VCS Chief Editors, Prof. Dr. Jürgen Dengler further comments on the latest achievements of the journal, while also highlighting particularly valued recent publications.
The team also uses the occasion to invite experts in the field of vegetation science to submit their manuscripts in 2024 to make use of the generous financial support by the IAVS. Given the increasing interest in VCS, the journal also invites additional linguistic editors, as well as reviewers who wish to join the Editorial Review Board.
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Keep yourself updated with news from Vegetation Classification and Survey on X (formerly Twitter) and Facebook. You can also follow IAVS on X and join the Association’s public group on Facebook.
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*Note that the Scopus database features a different selection of scientific journals compared to Web of Science to estimate citation metrics. The indexers are also using different formulae, where the former looks into citations made in the last two complete years for eligible papers published in the same years.
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About Vegetation Classification and Survey:
Vegetation Classification and Survey (VCS) is an international, peer-reviewed, online journal on plant community ecology published on behalf of the International Association for Vegetation Science (IAVS). It is devoted to vegetation survey and classification at any organisational and spatial scale and without restriction to certain methodological approaches.
The scope of VCS is focused on vegetation typologies and vegetation classification systems, their methodological foundation, their development and their application. The journal publishes original papers that develop new typologies as well as applied studies that use such typologies, for example, in vegetation mapping, ecosystem modelling, nature conservation, land use management, or monitoring. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping, such as algorithms, databases and nomenclatural principles, or are dealing with the conceptual and theoretical bases of vegetation survey and classification.
VCS also includes two permanent collections (or sections): “Ecoinformatics” and “Phytosociological Nomenclature”.
About Pensoft:
Pensoft is an independent, open-access publisher and technology provider, best known for its biodiversity journals, including ZooKeys, Biodiversity Data Journal, Phytokeys, Mycokeys, One Ecosystem, Metabarcoding and Metagenomics and many others. To date, the company has continuously been working on various tools and workflows designed to facilitate biodiversity data findability, accessibility, discoverability and interoperability.
About ARPHA Platform:
Pensoft publishes its journals on its self-developed ARPHA publishing platform: an end-to-end, narrative- and data-integrated publishing solution that supports the full life cycle of a manuscript, from authoring to reviewing, publishing and dissemination. ARPHA provides accomplished and streamlined production workflows that can be heavily customised by client journals not necessarily linked to Pensoft as a publisher, since ARPHA is specially targeted at learned societies, research institutions and university presses. The platform enables a variety of publishing models through a number of options for branding, production and revenue models. Alongside its elaborate and highly automated publishing tools and services, ARPHA provides a range of human-provided services, such as science communication and assistance in indexation at databases like Web of Science and Scopus, to provide a complete full-featured publishing solution package.
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.
With more than 30,000 native plant species, including thousands found nowhere else on Earth, China is known for its abundant flora. New species are frequently discovered in the country due to its size and variety of ecosystems.
These five new species with distinct flowers were recently published in Pensoft’s open-access journal PhytoKeys.
Belonging to the daisy family (Asteraceae), Melanoseris penghuana was observed growing on steep grassy slopes along the valley edge of Jiulonggou, Mt. Jiaozi Xueshan, at an elevation of approximately 3,200 m.
Through data analysis from two field surveys, the conservation status of this species was classified as Vulnerable. However, located within the Jiaozi Xueshan National Nature Reserve where human disturbance is minimal, its habitat is relatively well protected.
Hydrangea xinfeniae belongs to the family Hydrangeaceae and was discovered in the Huagaoxi National Nature Reserve in Shuiwei Town, Sichuan Province. It grows on moist soils under the broadleaved forest at an elevation of 1,200–1,300 m.
Currently known from only three relatively small populations of the type locality, its conservation status is assessed as Data Deficient.
This new species of cherry blossom belongs to the rose family (Rosaceae). It is currently known only from Wuyishan National Park, Fujian and Jiangxi Province, where it grows in various habitats such as the margins of evergreen broad-leaved forests, valleys, or roadsides, at an altitude of 600–1,000 m.
Belonging to the madder family (Rubiaceae), Ophiorrhiza reflexa grows in moist areas under evergreen broad-leaved forests in the limestone region of Napo County, Guangxi.
Researchers found three populations of the species with more than 1,000 individuals at each site during field investigations. The three sites all belong to Laohutiao Provincial Nature Reserve, which is well-protected and not under threat. Ophiorrhiza reflexa is preliminarily assessed as Least Concern.
Ligularia lushuiensis belongs to the daisy family (Asteraceae). It is currently known only from its type locality, Lushui, northwestern Yunnan, where it grows in alpine meadows at an elevation of 3,322 m.
Currently known only from a small population at its type locality, the single population researchers discovered consists of no more than 200 mature individuals. Overgrazing may threaten the habitat of this species, and it has been preliminarily categorised as Critically Endangered.
A post on social media asked about plant genera named for women and sparked a lively discussion with many contributors. This simple question was not as easily answered as initially thought. The resulting informal working group tackled this topic remotely during the COVID-19 pandemic and beyond. The team was motivated by the desire to amplify the contribution of women to botany through eponymy. The work of this team has so far resulted in a paper in Biodiversity Data Journal, presentations at several conferences, and a linked open dataset.
Prior to our international collaboration, no dataset was available to answer these simple questions and the required information was scattered in many different data sources. We set out to bring these data together and in doing so developed and refined our workflow. Our data paper documents this innovative workflow bringing together the various data elements needed to answer our research questions. Ultimately we created a Linked Open Data (LOD) dataset that amplified the names of women and female mythological beings celebrated through generic names of flowering plants.
🙋🏻♀️Inspired by the melastome plant genus 𝘔𝘦𝘳𝘪𝘢𝘯𝘪𝘢: which plant genera do you know that honor women? Who were/are they? 🌺 ¿Qué géneros de plantas dedicados a mujeres conoces? ¿Quienes fueron/son? 🧵👇🏽 #WomenInSTEMhttps://t.co/QWpyaMfihTpic.twitter.com/XBCYD6hmx1
During our research process we focused on pulling data from a wide variety of sources while at the same time proactively sharing the data generated as widely as possible. This was done by adding and linking it to multiple public databases and sources (push-pull) including the International Plant Name Index (hereafter IPNI), Tropicos®, Wikidata, Bionomia and the Biodiversity Heritage Library (hereafter BHL).
Visualisation of our workflow to create a working list of flowering plant genera named for women.
For our list of genera, each of the protologues were reviewed to confirm the etymology or eponymy. To find the generic prologues, we searched botanical databases such as IPNI and Tropicos, openly accessible providers of digital publications and other digital libraries and websites that provide free access to such publications. Here the BHL was invaluable as the majority of protologues and many other relevant publications were openly accessible through this digital library. Where no digital publication was available we accessed scientific literature through our affiliated institutions.
For the women, our starting point was the “Index of Eponymic Plant Names – Extended Edition” by Lotte Burkhardt (2018). We manually extracted all genera honouring women. This dataset was supplemented with other sources including IPNI (2023), Mari Mut (2017-2021), a 2022 updated version of Burkhardt’s document (Burkhardt 2022), as well as suggestions received from colleagues and generated from our own research.
We collected the following information as structured data: information on the woman honoured, the genera named in honour of the woman, the year and place of the protologue or original publication (the nomenclatural reference), the author(s) of the genus name, and the link to the protologue or original publication if available online.
Wikidata
Wikidata was the central data repository and linking mechanism for this project as it provided structured data that can be read and edited by humans and machines and it acts as a hub for other identifiers. As such Wikidata played a central role in semantic linking and enriching of our data.
Wikidata items for the plant genera were created or enriched with information about the name, the author(s) of the genus and the year of publication. Those statements were referenced using the original publication. If the protologue was available on BHL, the BHL bibliographic or page number was added to that reference, thus creating a digital link improving access to the protologue. While undertaking this work we also collated a list of all those public domain publications that appeared to be absent from BHL. We passed on this list to BHL and requested these texts be scanned and added to BHL for the benefit of everyone.
We then added a named afterstatement to the Wikidata item for the appropriate plant genera linking that item to the Wikidata item for the woman honoured. Wikidata items for the women honoured were newly created or enriched. We researched each person and her contributions, plus information on mythological figures where necessary, and added this information to Wikidata items. Our work also included disambiguating the woman from other people with identical or similar names.
To amplify the women’s contributions to science and to enrich the wider (biodiversity) data ecosystem, we linked to other Wikidata items and websites or databases by adding other relevant identifiers. For example if the women were botanists, botanical collectors or other naturalists, we used the author property to link the women to publications written by them. In addition, we added the women to Bionomia and attributed specimens collected or identified by them to their profiles.
Our work also included enriching Wikidata items of taxon authors. IPNI and Tropicos were searched for these author names, and websites such as BHL, the Global Biodiversity Information Facility (GBIF) or other specialist databases were consulted. Corrections or newly researched information on taxon authors was placed not just in Wikidata but was also sent together with the corresponding references to IPNI and Tropicos. This information was then used by those organizations to update these databases accordingly.
As a result of our data being placed in Wikidata it is available to be queried via the Wikidata Query Service.
Our Goal Achieved
As a result of our project, we published a dataset of 728 genera honouring women or female beings. This was a nearly twenty-fold increase in the number of genera linked to women in Wikidata. Our analysis paper on this data is forthcoming.
Notable Women
Monsonia L.
All of us came away from this research with a favourite story. One that stood out was Ann Monson, for whom Linnaeus named Monsonia. Linnaeus wrote a delightful letter to her about their creating, platonically of course, a kind of plant love-child between them, in the form of this new genus.
Translated from Latin: “….Lock these [seeds] in a pot, and place them in the window of the chamber towards the sun, when it bursts forth in February, and in the first summer the sun blooms and lasts the most beautiful Alstromeria, which no one has seen in England, and you bring forth no flowers. If it should come to pass, as I wish, if you offer our flames, I would only wish to beget with you an only child, as a pledge of my love, little Monsonia, by which you may perpetuate the fame of Lady in the kingdom of Flora, who was the Queen of Women.”
Fittonia Coem.
Two eponymous women with an interesting story are Sarah Mary Fitton and her sister Elizabeth. They wrote Conversations on Botany in 1817 accompanied by colour engravings of flowers which popularised botany with women. The genus Fittonia was named in their honour.
Chanekia Lundell
Another woman honoured in a plant genus was Mercedes Chanek, a Mayan plant collector who worked in the 1930’s for Cyrus Longworth Lundell and collected for the University of Michigan in British Honduras, today Belize. Very little is known about her life and work. However, her collections are detailed in Tropicos and Bionomia, and you can see the genus named for her by Lundell in IPNI under Chanekia.
An example of a mythological female being honoured in several plant names is that of Medusa, who has the most genera named after her, six, more than any real woman!
We hope that our data paper inspires others to use the methodology and workflow described to create other linked open datasets, e.g. celebrating and amplifying the contributions of underrepresented or marginalised groups in science.
Data paper:
von Mering S, Gardiner LM, Knapp S, Lindon H, Leachman S, Ulloa Ulloa C, Vincent S, Vorontsova MS (2023) Creating a multi-linked dynamic dataset: a case study of plant genera named for women. Biodiversity Data Journal 11: e114408. https://doi.org/10.3897/BDJ.11.e114408
Today, 16 September 2023, we are celebrating our tenth anniversary: an important milestone that has prompted us to reflect on the incredible journey thatBiodiversity Data Journal (BDJ) has been through.
From the very beginning, our mission was clear: to revolutionise the way biodiversity data is shared, accessed, and harnessed. This journey has been one of innovation, collaboration, and a relentless commitment to making biodiversity data FAIR – Findable, Accessible, Interoperable, and Reusable.
Over the past 10 years, BDJ, under the auspices of our esteemed publisher Pensoft, has emerged as a trailblazing force in biodiversity science. Our open-access platform has empowered researchers from around the world to publish comprehensive papers that seamlessly blend text with morphological descriptions, occurrences, data tables, and more. This holistic approach has enriched the depth of research articles and contributed to the creation of an interconnected web of biodiversity information.
In addition, by utilising ARPHA Writing Tool and ARPHA Platform as our entirely online manuscript authoring and submission interface, we have simplified the integration of structured data and narrative, reinforcing our commitment to simplifying the research process.
One of our most significant achievements is democratising access to biodiversity data. By dismantling access barriers, we have catalysed the emergence of novel research directions, equipping scientists with the tools to combat critical global challenges such as biodiversity loss, habitat degradation, and climate fluctuations.
We firmly believe that data should be openly accessible to all, fostering collaboration and accelerating scientific discovery. By upholding the FAIR principles, we ensure that the datasets accompanying our articles are not only discoverable and accessible, but also easy to integrate and reusable across diverse fields.
As we reflect on the past decade, we are invigorated by the boundless prospects on the horizon. We will continue working on to steer the global research community towards a future where biodiversity data is open, accessible, and harnessed to tackle global challenges.
Ten years of biodiversity research
To celebrate our anniversary, we have curated some of our most interesting and memorable BDJ studies from the past decade.
Recently, news outlets were quick to cover a new species of ‘snug’ published in our journal.
“Life Beneath the Ice”, a short musical film about light and life beneath the Antarctic sea-ice by Dr. Emiliano Cimoli
We extend our heartfelt gratitude to our authors, reviewers, readers, and the entire biodiversity science community for being integral parts of this transformative journey. Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.
With expertise in science communication, dissemination and exploitation, Pensoft is involved in this project set to develop new technologies for monitoring species and their habitats across Europe
With expertise in science communication, dissemination and exploitation, Pensoft became part of this project dedicated to new technologies for species and habitat monitoring across Europe
Background
The European Union puts a great value in monitoring the health of ecosystems, as comprehensive mapping can aid policy makers’ work in adopting appropriate legislation for nature conservation. It allows for understanding the impact of human activities and making informed decisions for effective management of nature’s resources. This is particularly important for the EU, as it has set ambitious goals to halt biodiversity loss and restore degraded ecosystems by 2030, as outlined in the EU Biodiversity Strategy for 2030.
Effective biodiversity monitoring can help the EU track progress towards these goals, assess the effectiveness of conservation policies and initiatives, and identify emerging threats to biodiversity.
Despite this awareness, efforts to monitor animals and plants remain spatially and temporally fragmented. This lack of integration regarding data and methods creates a gap in biodiversity monitoring, which can negatively impact policy-making. Today, modern technologies such as drones, artificial intelligence algorithms, or remote sensing are still not widely used in biodiversity monitoring.
MAMBO project (Modern Approaches to the Monitoring of BiOdiversity) recognises this need and aims to develop, test, and implement enabling tools for monitoring conservation status and ecological requirements of species and habitats. Having started in late 2022, the project is set to run for four years until September 2026.
Pensoft – with its proven expertise in communicating scientific results – is committed to amplifying the impact of MAMBO. Pensoft supports the project through tailored approaches to communication, dissemination and exploitation so as to reach the most appropriate target audience and achieve maximum visibility of the project.
Deep-dive into the project
In order to enrich the biodiversity monitoring landscape, MAMBO will implement a multi-disciplinary approach by utilising the technical expertise in the fields of computer science, remote sensing, and social science expertise on human-technology interactions, environmental economy, and citizen science. This will be combined with knowledge on species, ecology, and conservation biology.
More specifically, the project will develop, evaluate and integrate image and sound recognition-based AI solutions for EU biodiversity monitoring from species to habitats as well as promote the standardised calculation and automated retrieval of habitat data using deep learning and remote sensing.
“Classification algorithms have matured to an extent where it is possible to identify organisms automatically from digital data, such as images or sound,”
“Technical breakthroughs in the realm of high spatial resolution remote sensing set the future of ecological monitoring and can greatly enrich traditional approaches to biodiversity monitoring.”
In order to achieve its goals, the project will test existing tools in combination with MAMBO-developed new technologies at the project’s demonstration sites geographically spread across Europe. This will contribute to an integrated European biodiversity monitoring system with potential for dynamic adaptations.
Pensoft is part of MAMBO’s Work Package 7 (WP7): “Science-policy interface and dissemination”, led by Helmholtz Centre for Environmental Research (UFZ). The work package is dedicated to providing a distinct identity of the project and its services through branding, visualisation and elaborated dissemination and communication strategy.
Within WP7, Pensoft will also be taking care after the launch of an open-science collection of research outputs in the scholarly journal Research Ideas and Outcomes(RIO).
Amongst the tasks of the partners in WP7 is also the development of different pathways for integrating new technologies and innovations into the EU Pollinators Monitoring Scheme (EU PoMS; SPRING).
You can find more about the project on the MAMBO website: mambo-project.eu. Stay up to date with the project’s progress on Twitter (@MAMBO_EU) and Linkedin (/MAMBO Project).
Costus prancei, one of the 18 newly described species in Costaceae.
I am a retired government bureaucrat who worked for 40 years as an administrator in state and federal taxation. I have absolutely no formal training in botany, but now I find myself as an active participant in a major taxonomic revision and a coauthor in the publication of 18 new species in a plant family called Costaceae. This is the story of how my gardening hobby turned into an avocation and led me to work with some of the premier botanists in the world. It is also the story of how I have met several other plant enthusiasts from countries throughout the tropics who have contributed so very much to our work. I write this story in the hopes of encouraging more professional scientists to incorporate the observations of such “citizen scientists” in their research, and to encourage these enthusiasts to more carefully document their observations and post their photos and notes to resources like Inaturalist.org.
Costus whiskeycola, one of the 18 newly described species in Costaceae.
My story started about 30 years ago when my wife gave me a rhizome of the white butterfly ginger (Hedychium coronarium) as a Christmas present. I became interested in gingers, species of the family Zingiberaceae, but soon my interests began to focus almost exclusively on the closely related “spiral gingers” in the family Costaceae. I loved the architecture of the plants with their spiral staircase of leaves leading up to a variety of shapes and colors of bracts and flowers. I started collecting any cultivated Costus plants I could find in nurseries or mail-order catalogues. Soon, I learned that only a few species can survive outdoors in the winter where I live, so built a greenhouse.
Costus convexus, one of the 18 newly described species in Costaceae.
My serious interest in Costaceae began after I obtained a copy of the 1972 monograph of New World Costaceae by Dr. Paul Maas. It became my bible.
As I studied his descriptions of the species and applied his identification keys to the cultivated plants, I soon realized that many of the popular Costus species in cultivation had been incorrectly identified. I started doing presentations to garden clubs and posting to online groups. I developed a website called “Gingers ‘R’ Us.”
My “real job” had me traveling to Washington, DC periodically and I always tried to carve out time to visit Mike Bordelon at the Smithsonian Greenhouses in Suitland, Maryland. On one of these trips, I met Dr. Chelsea Specht, who was working at the Smithsonian Institution as a postdoctoral fellow.
Chelsea Specht and Mike Bordelon at the Smithsonian Greenhouses in 2004.
She had written what I believe is the first molecular study in Costaceae in 2001.This opened up a whole new world of interest for me as I tried to understand these new-to-me terms, like “clades” and “phylogenetic relationships”. In this paper she introduced the new generic divisions of the family that were solidified five years later in a more complete phylogenetic study . Chelsea very patiently answered my novice questions about phylogenetic trees and how they relate to the taxonomy of the plants.
Reinaldo Aguilar in 2013 at the type locality of Costus maritimus, now a synonym in the Costus comosus complex.
In 2005 I made my first trip to the New World tropics looking for Costus in its native habitat. On the Osa Peninsula of Costa Rica, I was incredibly lucky to meet Reinaldo Aguilar, the world-famous “para-taxonomist” who has studied the plants of the Osa for over 30 years. He is is self-taught like me and does not have a botanical degree, but has coauthored many scientific articles. He worked closely with the late Scott Mori of the New York Botanical Garden and was honored in a 2017 article in NYBG Science Talk.
That first trip to Costa Rica had me hooked. I fell in love with tropical forests and over the next few years made trips to several other Latin American countries as well as back to Costa Rica. Always, my focus was on Costus and the other members of its family.
Along the way, I met several “unsung heroes” in the plant world, like Marco Jiménez Villata, whom I met in the town of Zamora in southern Ecuador. Marco specializes in orchids, but he is also a generalist and knows a lot about the plants of southern Ecuador. He (now retired) was a school administrator and had traveled to many remote villages in the province and was always on the lookout for interesting plants. I have traveled with Marco and his son Marco Jiménez León several other times and we have become good friends.
Marco Jimenez and son Marco with Costus convexus.
In 2015 we went to the type locality of the species Costus zamoranus and took the first photographs of this species. At that trip, Marco showed me an area of high elevation near the Podocarpus National Park, where I found an unusual-looking Costus that we are now describing as Costus oreophilus. He also showed me unexplored places where I found another new species, Costus convexus. I made sure we credited him with his role in the discovery and documentation of those new species in our publication in PhytoKeys.
I have also traveled several times in Panama and Ecuador with another very well known, but non-doctorate plant enthusiast – Carla Black. Carla is the president of the Heliconia Society International, an organization uniting enthusiasts (scientists and non-scientists) in the order Zingiberales.
Carla Black with Juan Carlos Amado on the old Camino Real.
In 2015 we searched for the critically endangered Costus vinosus. We found a few plants growing deep in the forest of the Chagres National Park along an old Spanish trail used to transport gold to the Atlantic coast. There is still a mystery regarding the true form of the flower of C. vinosus, and I am in touch with another Inaturalist observer who has found it (not in flower) in the mountains northeast of Panama City. He will let me know when he finds it in flower!
Costus callosus, one of the 18 newly described species in Costaceae.
In 2019 Carla and I visited the “Willie Mazu” site in Panama to photograph and study the new species Costus callosus, and in Santa Fé de Veraguas, we looked for a species proposed by Dr. Maas that is now described as Costus alleniopsis.
My serious collaboration with Dr. Maas began in 2017, when I was preparing for a trip to Oaxaca in southern Mexico. He asked me to be on the lookout for two species of Costus from that region that he had identified as new based solely on his examination of herbarium specimens, without any good data on the floral parts.
By that time, I was posting my Costus observations on Inaturalist.org and using that resource to look for interesting plants. I also used it to find plant people to contact for local information. For this Mexico trip I found a huge number of observations posted by Manuel Gutiérrez from Oaxaca City.
Manuel Gutiérrez photographing the plant that turned out to be Costus sepacuitensis.
I found that he had extensive knowledge of the Chinantla region in the mountains east of Oaxaca City and had worked with the indigenous tribe there. Together, we explored the indigenous lands of Santa Cruz Tepetotutla.
We found many plants in flower of what Dr. Maas wanted to describe as Costus alticolus. We also found the species he planned to describe as Costus oaxacus, but I later found the same species in Guatemala, already described as Costus sepacuitensis.
Later I learned of the plans to prepare a complete revision to the taxonomy of the New World Costaceae. Together with Paul and Hiltje Maas, we spent several days at the Naturalis Herbarium in Leiden, comparing my photos against the hundreds of Costus herbarium specimens there. I had a long list of species that was curious about, and we were able to get through it and figure out what questions remained, even though we had not come up with all the answers.
Dave Skinner and Paul Maas discussing some Costus spp. in Leiden in 2017.
It was soon apparent that there are major changes needed in the taxonomy and nomenclature of these plants, and that information from the field would be an essential supplement to the observations made from the herbarium specimens.
Paul and Hiltje Maas in Leiden in 2017.
In 2016 I visited the type locality of Costus laevis in central Peru. I was surprised to find that the plants there are nothing at all like the Costus laevis of Central America, but match perfectly to the herbarium specimen that was deposited in Spain over 230 years ago. It was clear to me that the herbarium specimen designated as the type had been misinterpreted. I wrote an article explaining the problem – but I had no idea what the solution might be.
Dr. Maas agreed that there was a problem with that species that we eventually resolved. This resolution will be a part of the forthcoming revision of the New World Costaceae that is in preparation, nearing completion.
Another major problem involved the Costus guanaiensis complex. Paul and Hiltje, along with Chelsea, had visited the New York Botanical Garden Herbarium, where the holotype of that species is held, and realized that it had been misinterpreted due to the lack of a good flower description. What had been identified as Costus guanaiensis in the herbarium was actually a completely different species that Maas had planned to describe as a new species.
Dave Skinner with a plant in cultivation of Costus gibbosus at Rio Palenque Science Center, Ecuador.
The entire C. guanaiensis complex needed name changes and redefinitions of species boundaries, ultimately resulting in the description of Costus gibbosus that is published in PhytoKeys. The resolution of the other members of that complex will be explained in the forthcoming revision. Over the next several years, Paul and I exchanged 1,626 emails (yes, I counted them – with the help of MS Outlook) pounding out the details of the changes needed in the taxonomy of New World Costaceae. In collaboration with him, I made many more field trips to resolve the remaining questions we had.
My extensive collaboration with Paul Maas has been one of the most rewarding experiences of my lifetime. He has taught me so much about the rules of nomenclature and the process of describing a new species. The one thing he could never teach me was his almost uncanny ability to look at a dried herbarium specimen and make a determination of the species. I suppose that only comes from experience as he has examined over 11,000 specimens of Costaceae that will become our list of exxicatae when the full revision is published.
I should not fail to mention my time working with Dr. Thiago André. In 2014 I flew to Rio de Janeiro and then Thi and I, along with his academic advisor and another student, went to the state of Espirito Santo to look for the endangered species Chamaecostus cuspidatus. Thi has been our expert in that genus and has helped with the review of the new species published in PhytoKeys, Chamaecostus manausensis. In 2014 he was still finishing his doctorate and was in process of preparing a molecular phylogeny and morphological study of the species complex of Chamaecostus subsessilis.
Thiago André with Chamaecostus cuspidatus in 2014.
Thi and I have stayed in close contact, and he came to Florida one year to visit in my home and see the Costaceae in my private garden, Le Jardín Ombragé. He is now a professor at the Universidade de Brasília.
Finally, I should discuss my collaboration with Eugenio Valderrama and the other members of the Specht Lab at Cornell University. In 2018 I went to Cornell to visit Eugenio and we discussed the sampling to be used in the molecular phylogeny that will be a very important part of the full revision when it is published.
Eugenio Valderrama and Chelsea Specht with Costus convexus.
At Cornell, Eugenio produced a novel baiting schema for extracting specific genes from across all Costus species and in 2020 published a paper. With further sampling, another paper was published in 2022 to reveal interesting data on a whole package of pollination-related characters, and how they show evidence of convergent evolution. Eugenio’s phylogenies very well support the new species we are publishing in PhytoKeys, and the full molecular phylogeny will be included in our full revision when it is published.
Eugenio checking out a Renealmia sp. Antioquia, Colombia 2022.
Just this past December I went to Colombia to attend the Heliconia Society Conference at Quindío, and Eugenio and I each made presentations there about our work with Costaceae. Then we traveled together to investigate several other interesting species of Costaceae, including the new species Costus antioquiensis, and a strange yellow bracted form of Costus comosus found in the species-rich area of San Juan de Arama in Meta.
How did I know to look there? An observer, a citizen scientist, had posted his records and photos on Inaturalist.org. I have my account set to filter all Costaceae and send me a daily email with all the new postings of the family, and this plant will now be appearing as a sample in a molecular phylogeny and as an observed species in a monograph.
I hope this blog article will provide some background and insight into what I think must be an unusual collaboration between a citizen scientist and the much more qualified lead authors of our PhytoKeys article describing eighteen new species in Costaceae. It has certainly been a rewarding experience for me, and I hope other plant enthusiasts will be encouraged to share their observations on forums like Inaturalist.org, providing detailed and accurate information and photos. At least for the one plant family I have some expertise in, I will continue to monitor and curate those observations on Inaturalist.
André T, Specht CD, Salzman S, Palma-Silva C, Wendt T (2015) Evolution of species diversity in the genus Chamaecostus (Costaceae): Molecular phylogenetics and morphometric approaches. Phytotaxa 204(4): 265-276. https://doi.org/10.11646/phytotaxa.204.4.3
Maas, P. J. M. (1972). Costoideae (Zingiberaceae). Flora Neotropica 8, 1–139. doi: 10.1093/aob/mch177
Maas PJM, Maas-van de Kamer H, André T, Skinner D, Valderrama E, Specht CD (2023) Eighteen new species of Neotropical Costaceae (Zingiberales). PhytoKeys 222: 75-127. https://doi.org/10.3897/phytokeys.222.87779
Salzman S, Driscoll HE, Renner T, André T, Shen S, Specht CD (2015) Spiraling into history: A molecular phylogeny and investigation of biogeographic origins and floral evolution for the genus Costus. Systematic Botany 40(1): 104–115. https://doi.org/10.1600/036364415X686404
Skinner D (2008) Costus of the Golfo Dulce Region. Heliconia Society Bulletin 14(4):1-6
Skinner D and Jiménez M (2015) Costus zamoranus: An endemic species to Zamora-Chinchipe Province in Southeastern Ecuador. Heliconia Society Bulletin 21(3):4-9
Skinner D (2016) Following Ruiz. Heliconia Society Bulletin 22(4): 7–14.
Skinner D and Black C. (2016) Search for the Mysterious Lost Plant (Costus vinosus). Heliconia Society Bulletin 22(3):1-3
Skinner D (2019) A Tale of Two Costus (Costus sepacuitensis) and Costus cupreifolius) Heliconia Society Bulletin 25(1):1-3
Specht CD, Kress WJ, Stevenson DW, DeSalle R (2001) A molecular phylogeny of Costaceae (Zingiberales). Molecular Phylogenetics and Evolution 21(3): 333–345. https://doi.org/10.1006/mpev.2001.1029
Specht CD, Stevenson DW (2006) A new phylogeny-based generic classification of Costaceae (Zingiberales). Taxon 55(1): 153–163. https://doi.org/10.2307/25065537
Valderrama E, Sass C, Pinilla-Vargas M, Skinner D, Maas PJM, Maas-van de Kamer H, Landis JB, Guan CJ, AlmeidaA., Specht CD (2020) Unraveling the spiraling radiation: A phylogenomic analysis of neotropical Costus L. Frontiers in Plant Science 11: 1195. https://doi.org/10.3389/fpls.2020.01195
Valderrama E, Landis JB, Skinner D, Maas PJM, Maas-van de Kamer H, Sass C, Pinilla-Vargas M, Guan CJ, Phillips R, Almeida A, Specht CD (2022) The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L.Frontiers in Plant Science 13: https://doi.org/10.3389/fpls.2022.874322
“In the present biodiversity crisis scenario, it is critical that we do not neglect basic scientific disciplines like taxonomy, since cataloguing biodiversity is a fundamental step towards its preservation.”
The knowledge of biodiversity in allegedly well-known places is not as complete as one would expect and its detailed study by researchers continues to offer surprises, is what we find out in a new study of the flora of south-central Spain.
Now, Spanish botanists from Pablo de Olavide University (Seville, Spain) have described a new plant species of the papyrus family (Cyperaceae) restricted to the La Mancha region in south-central Spain. This region is in fact well-known for classic literary fans, who might recognise the name as the main setting in Miguel de Cervantes’ (1547–1616) masterpiece Don Quixote.
Artistic recreation depicting Don Quixote and his squire Sancho Panza with the iconic La Mancha windmills, and a Carex quixotiana’s habitat. Image by Faro Míguez.
The epic novel, which tells the story of the life and journeys of Alonso Quijano, a Spanish hidalgo (nobleman), who becomes the knight-errant Don Quixote de la Mancha, is commonly considered to be one of the greatest literary works ever written, with its number of editions and translations thought to be only surpassed by those of the Bible.
The new species, now scientifically known as Carex quixotiana, belongs to sedges of the genus Carex, a group of herbs included in the papyrus family (Cyperaceae). The classification (taxonomy) of these plants is difficult, as it is a highly diverse and widely distributed genus, whose species are frequently hard to tell apart. In fact, C. quixotiana has itself evaded the eyes of expert botanists for decades, because of its close resemblance to related species.
“Cryptic species are frequent in complex plant groups, such as sedges, and integrative studies encompassing different data sources (e.g. morphology, molecular phylogeny, chromosome number, ecological requirements) are needed to unravel systematic relationships and accurately describe biodiversity patterns,”
says Dr. Martín-Bravo, senior author of the paper.
After a preliminary genetic study pointed to something odd about specimens of what was later to be known as Carex quixotiana, the authors set off on exhaustive field collecting campaigns across La Mancha. As they studied additional populations of the plant in further detail, using morphology, phylogenetics, and chromosome number, the scientists confirmed that they were looking at a species previously unknown to science. Understandably, the distribution range of the newly discovered species, restricted to the mountain ranges surrounding La Mancha (Sierra Madrona and Montes de Toledo), made the authors think about Cervantes’ masterpiece.
So far only known from 16 populations, Carex quixotiana prefers habitats with high water availability, such as small streams, wet meadows and riverside (riparian) forests.
Since little is known about the species’ demographics, including the number of mature individuals in the wild, further investigation is required to determine its conservation status. However, based on what they have learnt so far about the species, the authors of the present study assume that:
“it is an Iberian endemic with a relatively small number of populations and distribution range, which would benefit from legal protection and inclusion in in-situ/ex-situ conservation programmes.”
“In the present biodiversity crisis scenario, it is critical that we do not neglect basic scientific disciplines like taxonomy, since cataloguing biodiversity is a fundamental step towards its preservation and, thus, sustainable management,”
say the researchers.
In conclusion, the scientists point to their results as yet another proof of how much there is still to learn about Earth’s biodiversity, even when it comes to supposedly well-known organisms, such as flowering plants, and countries, whose flora is presumed to be fully documented. The “Flora Iberica”, for example, which covers Spain and Portugal, has only recently been finalised, the team reminds us.
Close-up images of reproductive parts (inflorescences known as spikes) of the newly described species Carex quixotiana. Photo by Modesto Luceño.
Research article:
Benítez-Benítez C, Jiménez-Mejías P, Luceño M, Martín-Bravo S (2023) Carex quixotiana (Cyperaceae), a new Iberian endemic from Don Quixote’s land (La Mancha, S Spain). PhytoKeys 221: 161-186. https://doi.org/10.3897/phytokeys.221.99234
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,”
