Spectacular subtropical montane forest scenery in Yushan National Park. Credit: Ms. Wen-Ling Tsai
Montane forests, known as biodiversity hotspots, are among the ecosystems facing threats from climate change. To comprehend potential impacts of climate change on birds in these forests, researchers set up automatic recorders in Yushan National Park, Taiwan, and developed an AI tool for species identification using bird sounds. Their goal is to analyze status and trends in animal activity through acoustic data.
Compared to traditional observation-based methods, passive acoustic monitoring using automatic recorders to capture wildlife sounds provides cost-effective, long-term, and systematic alternative for long-term biodiversity monitoring.
The authors deployed six recorders in Yushan National Park, Taiwan, a subtropical montane forest habitat with elevations ranging from 1,200 to 2,800 meters. From 2020 to 2021, they recorded nearly 30,000 hours of audio files with abundant biological information.
An automatic recorder was installed on a tree to capture the surrounding soundscape. Credit: Ph.D. Candidate Shih-Hung Wu
However, analyzing this vast dataset is challenging and requires more than human effort alone.
To tackle this challenge, the authors utilized deep learning technology to develop an AI tool called SILIC that can identify species by sound.
SILIC can quickly pinpoint the precise timing of each animal call within the audio files. After several optimizations, the tool is now capable of recognizing 169 species of wildlife native to Taiwan, including 137 bird species, as well as frogs, mammals, and reptiles.
In this study, authors used SILIC to extract 6,243,820 vocalizations from seven montane forest bird species with a high precision of 95%, creating the first open-access AI-analyzed species occurrence dataset available on the Global Biodiversity Information Facility. This is the first open-access dataset with species occurrence data extracted from sounds in soundscape recordings by artificial intelligence.
The Gray-chinned Minivet (left) displays a secondary non-breeding season peak (right) which is possibly related to flocking behavior. Credit: Shih-Hung Wu, Ph.D. Candidate
The dataset unveils detailed acoustic activity patterns of wildlife across both short and long temporal scales. For instance, in diel patterns, the authors identify a morning vocalization peak for all species. On an annual basis, most species exhibit a single breeding season peak; however, some, like the Gray-chinned Minivet, display a secondary non-breeding season peak, possibly related to flocking behavior.
As the monitoring projects continue, the acoustic data may help to understand changes and trends in animal behavior and population across years in a cost-effective and automated manner.
The sound of Gray-chinned Minivet. Credit: Ph.D. Candidate Shih-Hung Wu
The authors anticipate that this extensive wildlife vocalization dataset will not be valuable only for the National Park’s headquarters in decision-making.
“We expect our dataset will be able to help fill the data gaps of fine-scale avian temporal activity patterns in montane forests and contribute to studies concerning the impacts of climate change on montane forest ecosystems,”
they say.
Original source:
Wu S-H, Ko JC-J, Lin R-S, Tsai W-L, Chang H-W (2023) An acoustic detection dataset of birds (Aves) in montane forests using a deep learning approach. Biodiversity Data Journal 11: e97811. https://doi.org/10.3897/BDJ.11.e97811
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The Cinereous Vulture (Aegypius monachus) – also known as Black Vulture, Monk Vulture or Eurasian Black Vulture – is the largest bird of prey in Europe.
Globally classified as Near Threatened, its populations in southern Europe, once abundant, have been experiencing a dramatic decline since the late 1800s. So dramatic, in fact, that by the mid-1900s, these birds had already been nowhere to be seen throughout most of their distributional range across the Old Continent. In Bulgaria, the species has been considered locally extinct since 1985.
Thanks to the re-introduction initiative that was started in 2015 by three Bulgarian non-governmental organisations: the leading and oldest environmental protection NGO in Bulgaria: Green Balkans, the Fund for Wild Flora and Fauna and the Birds of Prey Protection Society, the species is now back in the country.
By mid-2022, the team imported a total of 72 individuals from Spain and European zoos, before releasing them in strategically-chosen sites in the Eastern Balkan Mountains and the Vrachanski Balkan Nature Park in Northwestern Bulgaria.
The team brought 63 immatures from Spain, where the birds had been found in distress and rehabilitated in aviaries. The other nine juveniles were captive-bred in zoos, and then released by means of hacking, which involves an artificial nest, from where the fledglings can gradually ‘’take off” to a life in the wild.
The re-introduction campaign to date is presented in a research article, published in the open-access Biodiversity Data Journal. There, the scientists led by Ivelin Ivanov (Green Balkans), report on and discuss the effectiveness and challenges of the different release methods and offer tips on the conservation and re-introduction.
For example, hacking proved to be inefficient for establishing an entirely new core (or nucleus) population of Cinereous Vultures in the Balkan Mountains in Bulgaria. It did not work for supplementing a small settled group of individuals either.
Instead, the team recommend the aviary method and delayed release, where captive-bred birds are introduced to the new locality after a period of acclimatisation, where the birds can gain life experience to the local environment.
“The Cinereous Vulture re-introduction establishment phase in Bulgaria in the two first release sites is running according to the plan, and the first results are satisfactory,”
the scientists comment.
“Two distinct nuclei are now created, and the species started breeding, which might be a reason to up-list it in the Red Data Book of Bulgaria from ’Extinct’ to ‘Critically Endangered.’”
These two newly created breeding nuclei of the Cinereous Vulture in Bulgaria are the second and third of their kind in the Balkan Peninsula.
“Following a dramatic decline throughout the 20th century for decades, the species had remained in only one breeding colony in Dadia-Lefkimi-Soufli Forest National Park in north-eastern Greece. Now, exchange between the three colonies will facilitate the exchange of individuals, ensure long-term stability, and give rise to the regional population,”
the authors of the study say.
However, the team points out that further monitoring and modelling and adaptive management are indispensable for the long-term persistence of the new national population. Now that there is already evidence that the imported vultures have been successfully breeding in Bulgaria, there is one step left before it can be officially confirmed that the Cinereous Vulture species has successfully re-established in the country. This conclusion can only be made after the core breeding populations begin to produce about ten chicks every year and after the locally fledged individuals begin to reproduce on their own. Such results are expected by 2030.
The re-introduction of the Cinereous Vulture is the latest in a series of conservation projects focused on birds of prey in Bulgaria.
First, in a programme that started in 2009, the Griffon Vulture was successfully re-introduced in Bulgaria after about 50 years of “extinction”. In fact, the team took a lot of the know-how and methods used in that project to apply in the present project. The success story was published in a research paper in the Biodiversity Data Journal in 2021.
In fact, the very same day in 2021 saw two publications in the Biodiversity Data Journal that reported on re-introduction successes involving birds of prey in Bulgaria, which had gone missing for decades. The second instance was the discovery of the first nesting Saker Falcons in twenty years
Both scientific publications are part of a dynamic ‘living’ collection, titled “Restoration of species of conservation importance”, whose aim is to collate publicly available research studies reporting on the reintroduction and/or restocking of animal and plant species of conservation importance around the world. The collection was inspired by the “International Scientific Conference on Restoration of Conservation-Reliant Species and Habitats” held in Sofia, Bulgaria, in 2020.
“The restoration of species is one of the most important conservation tools in the context of constantly intensified human-driven global biodiversity loss. The reintroduction/restocking activities are related to significant research and data gathering before and during the work process, which ensures their sustainable success,”
explain the collection editors.
Research article:
Ivanov I, Stoynov E, Stoyanov G, Kmetova–Biro E, Andevski J, Peshev H, Marin S, Terraube J, Bonchev L, Stoev IP, Tavares J, Loercher F, Huyghe M, Nikolova Z, Vangelova N, Stanchev S, Mitrevichin E, Tilova E, Grozdanov A (2023) First results from the releases of Cinereous Vultures (Aegypius monachus) aiming at re-introducing the species in Bulgaria – the start of the establishment phase 2018–2022. Biodiversity Data Journal 11: e100521. https://doi.org/10.3897/BDJ.11.e100521
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Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data
The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications*submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge.
BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.
Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.
The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions,and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
To be eligible for the collection, a manuscript must comply with at least two of the conditions listed below. In the submission form, the author needs tospecify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.
All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.
Conditions for publication in the article collection:
The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)
Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.
Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.
Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.
More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin.
In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision or catalogue. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.
Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.
Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.
Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.
Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.
Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.
We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection:
Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data:
(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined?
(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)?
(4) How could research data and narratives be re-used to support more extensive and data-rich studies?
(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?
Once published, specimen records data are being exported in Darwin Core Archive to GBIF.
The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.
All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.
* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.
Follow the BiCIKL Project on Twitter and Facebook.Join the conservation on via #BiCIKL_H2020.
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OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
For the first time, the satellite tracks of two Antarctic blue whales, tagged a decade ago, have been published in the open-access Biodiversity Data Journal.
Ten years ago, Dr Virginia Andrews-Goff was riding the bowsprit of a six-metre boat, as a 30-metre, 120-tonne Antarctic blue whale surfaced alongside.
That day in the Southern Ocean, she became the first and, so far, the only person, to deploy satellite tags on two of these critically endangered and rarely sighted giants.
At the time, her success added weight to a case in the United Nations International Court of Justice, demonstrating that scientific research on whales could be conducted without killing them.
Dr Andrews-Goff and her colleagues at the Australian Antarctic Division have now published the two satellite tracks generated by that 2013 work, in the open-access Biodiversity Data Journal.
This is a unique data set that was incredibly challenging to get.
Dr Virginia Andrews-Goff
The tracks give an insight into the animals’ movement and behaviour on their feeding grounds, and illustrate the significant logistical challenges needed to successfully locate, tag, and track Antarctic blue whales.
“This is a unique data set that was incredibly challenging to get, and, unfortunately, for 10 years no-one has been able to generate more data,” Dr Andrews-Goff said.
“We know very little about the movement and distribution of Antarctic blue whales, where they migrate, where they forage and breed, and we don’t understand the threats they might face as they recover from whaling.”
Part of the issue is that the animals are incredibly difficult to find. Commercial whaling in the 1960s and ‘70s killed about 290,000 Antarctic blue whales, accounting for 90% of the population. By the late 1990s, the world’s population of Antarctic blue whales was estimated at 2280 animals.
Back in 2013, the research team used novel acoustic tracking techniques to detect blue whale calls and hone in on their location from up to 1000 kilometres away. Once the whales were in sight (in two separate locations), an expert crew manoeuvred close to their fast-moving targets.
The satellite tags showed that the whales travelled 1390 kilometres in 13 days and 5550 kilometres in 74 days, with an average distance of more than 100 kilometres per day.
“The two whales did entirely different things, but what became obvious is that these animals can travel really quickly,” Dr Andrews-Goff said.
“If you consider how far and fast these animals moved, protecting the broader population against potential threats will be tricky because they could potentially circumnavigate Antarctica within a single feeding season.”
Since the tracks were obtained, new analytical methods have added some behavioural context to the data.
Two movement rates were observed – a faster ‘in transit’ speed averaging 4.2 km/hr and a slower speed of 2.5 km/hr, thought to correspond with searching or foraging.
“It looks like the whales might hang around in one area to feed and then move quickly to another area and hang around there for another feed,” Dr Andrews-Goff said.
“There may be certain areas that are better feeding grounds than others. From a management perspective, it would be good to understand what is it that makes these areas important?”
Even at a sample size of two, Dr Andrews-Goff said the satellite tracks will assist the International Whaling Commission’s management of Antarctic blue whales, by providing initial insights into blue whale foraging ecology, habitat preferences, distribution, movement rates, and feeding. These will inform an in-depth assessment of Antarctic blue whales due to begin in 2024.
Original source:
Andrews-Goff V, Bell EM, Miller BS, Wotherspoon SJ, Double MC (2022). Satellite tag derived data from two Antarctic blue whales (Balaenoptera musculus intermedia) tagged in the east Antarctic sector of the Southern Ocean. Biodviersity Data Journal 10: e94228 https://doi.org/10.3897/BDJ.10.e94228
***
Conditions of Use – strictly non-commercial, once only, no archive + no sales The Australian Antarctic Division welcomes your interest in Australia’s Antarctic Program. The Commonwealth of Australia, represented by the Australian Antarctic Division of the Department of Climate Change, Energy, the Environment and Water (Commonwealth), hereby consents to you publishing each item of material listed below ONCE ONLY on a non-commercial, royalty-free and non-exclusive basis. Where material is published in a printed or electronic format (including on the internet), you are requested to acknowledge the photographer or videographer as listed below. If used on social media please tag the Australian Antarctic Division @AusAntarctic #AusAntarctic
This Consent does not entitle you to use the material specified below in any future article, feature or broadcast without further specific prior written permission of the Commonwealth or to adapt, modify, exploit or sublicense the material specified below in any way. By using this material, you agree to the terms of this Consent.
A new insect species from Kosovo challenges the idea of the intelligence and cleverness of humankind, compared to other organisms, with its scientific name.
Type locality of the new species. Photo by Halil Ibrahimi
Lying at the center of the Balkan Peninsula, Kosovo harbors a diversity of ecosystems and conditions, which have favored processes leading to the existence of many endemic and rare species. In the past few years, several new species of aquatic insects have been discovered from the small Balkan country, making it unique in terms of biodiversity. Unfortunately, as elsewhere in the Balkans, many of these ecosystems have deteriorated heavily.
A team of scientists from Kosovo, led by Professor Halil Ibrahimi of the University of Prishtina, recently found a new species of aquatic insect, a caddisfly, from the Sharr Mountains in Kosovo, and named it Potamophylax humoinsapiens.
The species epithet humoinsapiens is a combination of two Latin words, “humo”, which in English means “to cover with soil, to bury,” and “insapiens,” meaning “unwise”. The researchers explain this name refers to the unwise and careless treatment of the habitats of the new species: hydropower plant, illegal logging and pollution have greatly degraded the area in the past years. “In some segments, whole parts of the Lepenc River are “buried” in large pipes,” they write in their study, which was published in the open-access Biodiversity Data Journal.
Potamophylax humoinsapiens. Photo by Halil Ibrahimi
“The species name ‘humoinsapiens’ ironically sounds like Homo insapiens, and this new species is right in calling us unwise,” thinks Prof. Ibrahimi. “With its actions, humankind has caused the extinction of many species of insects and other organisms during the past decades and has degraded greatly all known ecosystems in the planet. The debate on questioning wise nature of humans is already ongoing.
In the past few years, Professor Halil Ibrahimi and his team have found several new species of aquatic insects from the Balkans, Middle East and North Africa. In an attempt to raise awareness for this group of vulnerable creatures, endangered greatly by human activities, the team of scientists has given their species unique names. One of their previous discoveries was named Potamophylax coronavirus in order to raise the attention to the silent and dangerous “pandemic” humans have caused in freshwater ecosystems in the Balkans.
The research team behind the discovery. Photo by Halil Ibrahimi
“By combining classical taxonomy and modern molecular analysis techniques with the unique names, we are making insect species talk to our collective consciousness. It is in humankind’s capacity to earn the name Homo sapiens again,” the researchers conclude.
Ibrahimi H, Bilalli A, Gashi A, Grapci Kotori L, Slavevska Stamenkovič V, Geci D (2023) Potamophylax humoinsapiens sp. n. (Trichoptera, Limnephilidae), a new species from the Sharr Mountains, Republic of Kosovo. Biodiversity Data Journal 11: e97969. https://doi.org/10.3897/BDJ.11.e97969
All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research.
As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service.
According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.
While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals.
This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.
“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”
said Robert Kiley, Head of Strategy at cOAlition S.
***
About cOAlition S:
On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.
About Plan S:
Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.
In 2018, NHM London’s digitisation team started a project to digitise non-type herbarium material from the legume family. A recent data paper in the Biodiversity Data Journal reports on the outcomes.
You can find the original blog post by the Natural History Museum of London, reposted here with minor edits.
Legumes are a group of plants that include soybeans, peas, chickpeas, peanuts and lentils. They are a significant source of protein, fibre, carbohydrates, and minerals in our diet and some, like the cowpea, are resistant to droughts.
The project’s outcomes were published in a data paper in the Biodiversity Data Journal. Within the project, the digitisation team aimed to collectively digitise non-type herbarium material from the legume family. This includes rosewood trees (Dalbergia), padauk trees (Pterocarpus) and the Phaseolinae subtribe that contains many of the beans cultivated for human and animal food.
Guinea, Ethiopia, Sudan, Kenya, Uganda, Tanzania, Mozambique, Malawi and Madagascar
Asian
Bangladesh, Myanmar, Nepal, New Guinea and India
Southern and Central American
Guatemala, Honduras, El Salvador, Nicaragua, Bolivia, Argentina and Brazil
ODA-listed Countries
The legume groups: Dalbergia, Pterocarpus and Phaseolinae,were chosen for digitisation to support the development of dry beans as a sustainable and resilient crop, and to aid conservation and sustainable use of rosewood and padauk trees. Some of these beans, especially cow pea and pigeon pea, are sustainable and resilient crops, as they can be grown in poor-quality soils and are drought stress resistant. This makes them particularly suitable for agricultural production where the growing of other crops would be difficult.
Digitally discoverable herbarium specimens can provide important information about the distribution of individual species, as well as highlighting which species occur naturally together.
While there have been collaborative efforts between herbaria in the past, these have tended to prioritise digitisation of type specimens: the example specimens for which a species is named.
Types are important to identification, but being individual specimens, they don’t offer insights into species distribution over time. By focusing on the non-types across the world and over the last 200 years, we have released a brand-new resource to the global scientific community.
Searching for beans
This collection was digitised by creating an inventory record for each specimen, attaching images of each herbarium sheet, and then transcribing more data and georeferencing the specimens, providing an accurate locality in space and time for their collection.
We originally had four months and three members of staff to digitise over 11,000 specimens. The Covid-19 lockdown was ironically rather lucky for this project as it enabled us to have more time to transcribe and georeference all of the records.
say the researchers behind the digitisation project.
Map showing breakdown of records by country.
“We were able to assign country-level data to 10,857 out of the total number of 11,222 records. We were also able to transcribe the collectors’ names from the majority of our specimen labels (10,879 out of 11,222). Only 770 out of the 2,226 individuals identified during this project collected their specimens in ODA listed countries. The highest contributors were: Richard Beddome (130 specimens), Charles Clarke (110), Hans Schlieben (98) and Nathaniel Wallich (79). The breakdown of records by ODA country can be seen in the chart below. “
Map showing breakdown of records by country and pie chart showing distribution by ODA listed countries.
From our data, we can see the peak decade of collection was the 1930s, with almost half (4,583 specimens or 49,43%) collected between 1900 and 1950 (Fig. 10).
This peak can be attributed to three of our most prolific collectors: Arthur Kerr, John Gossweiler and Georges Le Testu, all of whom were most active in the 1930s. The oldest specimen (BM013713473) was collected by Mark Catesby (1683-1749) in the Bahamas in 1726.
they explain.
An interesting, but perhaps unsurprising, finding is that our collection is strongly male-dominated.
There are only two women (Caroline Whitefoord and Ynes Mexia) in the list of our top 50 plant collectors and they are not close to the most prolific collectors.
We identified more women in the rest of our records, but their contribution is on average less than 25 specimens per person in the dataset consisting of more than 10,000 specimens. In contrast, the top five male collectors contributed 10% of our collection.
they continued
Releasing Rosewoods
Both the Pterocarpus and Dalbergia genera include species that are used as expensive good quality timber that is prone to illegal logging. Many species such as Pterocarpus tinctorius are also listed on the International Union for Conservation of Nature (IUCN) Red List of Threatened Species. By releasing this new resource of information on all these plants from three of the biggest herbaria in the world, we can share this datа with the people who are taking care of biodiversity in these countries. The data can be used to identify hotspots, where the tree is naturally growing and protect these areas. These data would also allow much closer attention to be paid to areas that could be targets for illegal logging activity.
Pterocarpus tinctorius is a species of padauk tree that is listed as endangered on the IUCN Red List.
Cowpea (Vigna unguiculata) is a food and animal feed crop grown in the semi-arid tropics.
The ODA-listed countries are economically impoverished and disproportionately prone to be disadvantaged with the changing climate whether from flood or drought or increase in temperature.
Using data to identify good, nutritious plant species that can be grown in such conditions can therefore benefit local communities, potentially reducing dependence on imports, aid and on less resilient crops.
the team adds in conclusion.
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This dataset is now openly available on the Museum’s Data Portal and a data paper about this work has been released in the Biodiversity Data Journal.
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The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”
The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft.
The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.
BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.
BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.
Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.
The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).
This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.
This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.
Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.
Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.
By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.
The Biodiversity Knowledge Hub is no longer existing on paper only! We are opening the 2nd day of the #BiCIKL_H2020 General Assembly looking at the prototype of the BKH created by the @LifeWatchERIC team. It's so exciting to see projects taking shape! 🤩 #Plovdivpic.twitter.com/RidzwBpxZx
“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”
said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.
“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”
Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.
“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”
Joe Miller, Executive Secretary and Director at GBIF, commented:
“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”
Joana Pauperio (biodiversity curator at EMBL-EBI) atthe 2nd General Assembly of the BiCIKL project.
“BiCIKL is leading data infrastructure communities through some exciting and important developments”
said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).
“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”
“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”
The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.
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Learn more about BiCIKL on the project’s website at: bicikl-project.eu
For the 37th time, experts from across the world to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
Between 17th and 21st October, about 400 scientists and experts took part in a hybrid meeting dedicated to the development, use and maintenance of biodiversity data, technologies, and standards across the world.
For the 37th time, the global scientific and educational association Biodiversity Information Standards (TDWG) brought together experts from all over the globe to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.
This was the first time the event happened in a hybrid format. It was attended by 160 people on-site, while another 235 people joined online.
The TDWG 2022 conference saw plenty of networking and engaging discussions with as many as 160 on-site attendees and another 235 people, who joined the event remotely.
“It’s wonderful to be in the Balkans and Bulgaria for our Biodiversity Information and Standards (TDWG) 2022 conference! Everyone’s been so welcoming and thoughtfully engaged in conversations about biodiversity information and how we can all collaborate, contribute and benefit,”
“Our TDWG mission is to create, maintain and promote the use of open, community-driven standards to enable sharing and use of biodiversity data for all,”
she added.
Prof Lyubomir Penev (Pensoft) and Deborah Paul (TDWG) at TDWG 2022.
“We are proud to have been selected to be the hosts of this year’s TDWG annual conference and are definitely happy to have joined and observed so many active experts network and share their know-how and future plans with each other, so that they can collaborate and make further progress in the way scientists and informaticians work with biodiversity information,”
said Pensoft’s founder and CEO Prof. Lyubomir Penev.
“As a publisher of multiple globally renowned scientific journals and books in the field of biodiversity and ecology, at Pensoft we assume it to be our responsibility to be amongst the first to implement those standards and good practices, and serve as an example in the scholarly publishing world. Let me remind you that it is the scientific publications that present the most reliable knowledge the world and science has, due to the scrutiny and rigour in the review process they undergo before seeing the light of day,”
he added.
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In a nutshell, the main task and dedication of the TDWG association is to develop and maintain standards and data-sharing protocols that support the infrastructures (e.g., The Global Biodiversity Information Facility – GBIF), which aggregate and facilitate use of these data, in order to inform and expand humanity’s knowledge about life on Earth.
It is the goal of everyone at TDWG to let scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused.
It is the goal of everyone volunteering their time and expertise to TDWG to enable the scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused by others. After all, biodiversity data underlie everything we know about the natural world.
If there are optimised and universal standards in the way researchers store and disseminate biodiversity data, all those biodiversity scientists will be able to find, access and use the knowledge in their own work much more easily. As a result, they will be much better positioned to contribute new knowledge that will later be used in nature and ecosystem conservation by key decision-makers.
On Monday, the event opened with welcoming speeches by Deborah Paul and Prof. Lyubomir Penev in their roles of the Chair of TDWG and the main host of this year’s conference, respectively.
The opening ceremony continued with a keynote speech by Prof. Pavel Stoev, Director of the Natural History Museum of Sofia and co-host of TDWG 2022.
Prof. Pavel Stoev (Natural History Museum of Sofia) with a presentation about the known and unknown biodiversity of Bulgaria during the opening plenary session of TDWG 2022.
He walked the participants through the fascinating biodiversity of Bulgaria, but also the worrying trends in the country associated with declining taxonomic expertise.
He finished his talk with a beam of hope by sharing about the recently established national unit of DiSSCo, whose aim – even if a tad too optimistic – is to digitise one million natural history items in four years, of which 250,000 with photographs. So far, one year into the project, the Bulgarian team has managed to digitise more than 32,000 specimens and provide images to 10,000 specimens.
The plenary session concluded with a keynote presentation by renowned ichthyologist and biodiversity data manager Dr. Richard L. Pyle, who is also a manager of ZooBank – the key international database for newly described species.
Keynote presentation by Dr Richard L. Pyle (Bishop Museum, USA) at the opening plenary session of TDWG 2022.
In his talk, he highlighted the gaps in the ways taxonomy is being used, thereby impeding biodiversity research and cutting off a lot of opportunities for timely scientific progress.
“There are simple things we can do to change how we use taxonomy as a tool that would dramatically improve our ability to conduct science and understand biodiversity. There is enormous value and utility within existing databases around the world to understand biodiversity, how threatened it is, what impacts human activity has (especially climate change), and how to optimise the protection and preservation of biodiversity,”
he said in an interview for a joint interview by the Bulgarian News Agency and Pensoft.
“But we do not have easy access to much of this information because the different databases are not well integrated. Taxonomy offers us the best opportunity to connect this information together, to answer important questions about biodiversity that we have never been able to answer before. The reason meetings like this are so important is that they bring people together to discuss ways of using modern informatics to greatly increase the power of the data we already have, and prioritise how we fill the gaps in data that exist. Taxonomy, and especially taxonomic data integration, is a very important part of the solution.”
Pyle also commented on the work in progress at ZooBank ten years into the platform’s existence and its role in the next (fifth) edition of the International Code of Zoological Nomenclature, which is currently being developed by the International Commission of Zoological Nomenclature (ICZN).
“We already know that ZooBank will play a more important role in the next edition of the Code than it has for these past ten years, so this is exactly the right time to be planning new services for ZooBank. Improvements at ZooBank will include things like better user-interfaces on the web to make it easier and faster to use ZooBank, better data services to make it easier for publishers to add content to ZooBank as part of their publication workflow, additional information about nomenclature and taxonomy that will both support the next edition of the Code, and also help taxonomists get their jobs done more efficiently and effectively. Conferences like the TDWG one are critical for helping to define what the next version of ZooBank will look like, and what it will do.”
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During the week, the conference participants had the opportunity to enjoy a total of 140 presentations; as well as multiple social activities, including a field trip to Rila Monastery and a traditional Bulgarian dinner.
TDWG 2022 conference participants document their species observations on their way to Rila Monastery.
While going about the conference venue and field trip localities, the attendees were also actively uploading their species observations made during their stay in Bulgaria on iNaturalist in a TDWG2022-dedicated BioBlitz. The challenge concluded with a total of 635 observations and 228 successfully identified species.
Amongst the social activities going on during TDWG 2022 was a BioBlitz, where the conference participants could uploade their observations made in Bulgaria on iNaturalist and help each other successfully identify the specimens.
“Biodiversity provides the support systems for all life on Earth. Yet the natural world is in peril, and we face biodiversity and climate emergencies. The consequences of these include accelerating extinction, increased risk from zoonotic disease, degradation of natural capital, loss of sustainable livelihoods in many of the poorest yet most biodiverse countries of the world, challenges with food security, water scarcity and natural disasters, and the associated challenges of mass migration and social conflicts.
Solutions to these problems can be found in the data associated with natural science collections. DiSSCo is a partnership of the institutions that digitise their collections to harness their potential. By bringing them together in a distributed, interoperable research infrastructure, we are making them physically and digitally open, accessible, and usable for all forms of research and innovation.
At present rates, digitising all of the UK collection – which holds more than 130 million specimens collected from across the globe and is being taken care of by over 90 institutions – is likely to take many decades, but new technologies like machine learning and computer vision are dramatically reducing the time it will take, and we are presently exploring how robotics can be applied to accelerate our work.”
In his turn, Dr Donat Agosti, CEO and Managing director at Plazi – a not-for-profit organisation supporting and promoting the development of persistent and openly accessible digital taxonomic literature – said:
“All the data about biodiversity is in our libraries, that include over 500 million pages, and everyday new publications are being added. No person can read all this, but machines allow us to mine this huge, very rich source of data. We do not know how many species we know, because we cannot analyse with all the scientists in this library, nor can we follow new publications. Thus, we do not have the best possible information to explore and protect our biological environment.”
Dr Donat Agosti demonstrating the importance of publishing biodiversity data in a structured and semantically enhanced format in one of his presentations at TDWG 2022.
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At the closing plenary session, Gail Kampmeier – TDWG Executive member and one of the first zoologists to join TDWG in 1996 – joined via Zoom to walk the conference attendees through the 37-year history of the association, originally named the Taxonomic Databases Working Group, but later transformed to Biodiversity Information Standards, as it expanded its activities to the whole range of biodiversity data.
“While this presentation is about TDWG’s history as an organisation, its focus will be on the heart of TDWG: its people. We would like to show how the organisation has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future?”,
Then, in the final talk of the session, Deborah Paul took to the stage to present the progress and key achievements by the association from 2022.
🤩Year in review by @idbdeb at #TDWG2022: many wonderful achievements & even more in the works!🙌 E.g.✅Memorandum of Understanding with Genomic Standards Consortium ✅new Mineralogy Task Group ✅new vision & mission statement ✅collaboration with @GBIF on the new data model.. 1/ pic.twitter.com/RZx8hlePOm
Deborah Paul reminds that – apart from the conference abstracts – the TDWG journal: Biodiversity Information Science and Standards (BISS) also welcomes full-lenght articles that demonstrate the development or application of new methods and approaches in biodiversity informatics.
Launched in 2017 on the Pensoft’s publishing platform ARPHA, the journal provides the quite unique and innovative opportunity to have both abstracts and full-length research papers published in a modern, technologically-advanced scholarly journal. In her speech, Deborah Paul reminded that BISS journal welcomes research articles that demonstrate the development or application of new methods and approaches in biodiversity informatics in the form of case studies.
Amongst the achievements of TDWG and its community, a special place was reserved for the Horizon 2020-funded BiCIKL project (abbreviation for Biodiversity Community Integrated Knowledge Library), involving many of the association’s members.
Having started in 2021, the 3-year project, coordinated by Pensoft, brings together 14 partnering institutions from 10 countries, and 15 biodiversity under the common goal to create a centralised place to connect all key biodiversity data by interlinking a total of 15 research infrastructures and their databases.
Deborah Paul also reported on the progress of the Horizon 2020-funded project BiCIKL, which involves many of the TDWG members. BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 key research infrastructures and their databases.
In fact, following the week-long TDWG 2022 conference in Sofia, a good many of the participants set off straight for another Bulgarian city and another event hosted by Pensoft. The Second General Assembly of BiCIKL took place between 22nd and 24th October in Plovdiv.
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You can also explore highlights and live tweets from TDWG 2022 on Twitter via #TDWG2022.
The Pensoft team at TDWG 2022 were happy to become the hosts of the 37th TDWG conference.
