Seven journals moving to ARPHA in early 2020 showcase the versatility of the publishing platform

Seven journals of diverse backgrounds, scopes and geographies are moving to Pensoft-developed open access publishing platform ARPHA.

A full-featured, open access publishing platform for journals, books and data, which comes with an extensive list of services and features – both automated and human-provided – to adapt to the individual needs of any client journal. But how does that translate into practice? 

The latest scholarly titles to join the ranks of ARPHA might just provide a perfect example of the capabilities of the platform to accommodate the specificity of scholarly journal across sciences, audiences, geographies and languages.

Amsterdam University Press strengthens partnership with ARPHA by launching two brand new journals

Journal of European Landscapes (JEL) and Heritage, Memory and Conflict Journal (HMC) add up to the partnership between ARPHA and Amsterdam University Press (AUP), which started in early 2018 with the transfer of the only Dutch-language open-access journal focussing on accountancy, business economics and related areas: Accountancy and Business Economics, or Maandblad voor Accountancy en Bedrijfseconomi (MAB).

Homepage of Amsterdam University’s journal Accountancy and Business Economics (Maandblad voor Accountancy en Bedrijfseconomi), using the white-label publishing solution of ARPHA Platform.

Not only was MAB the first journal on the platform that publishes articles exclusively in a language other than English, but also became an impressive precedent with its nearly 100-year content that got successfully dusted off and fitted into the user-friendly digital environment of today. All papers ever issued in MAB since its launch in 1923, were re-published, so that each could be assigned with a DOI; have its metadata registered on CrossRef; and its article content fully searchable within the PDF copy.

All three make use of ARPHA’s white-label publishing solution, which allows for AUP to carry its recognisable logo through a unified banner across the websites of the journals. Unlike MAB, however, JEL and HMC are to have their articles published exclusively in English to further promote their international scope and focus.

Heritage, Memory and Conflict Journal (HMC)

Homepage of the new Heritage, Memory and Conflict Journalpublished by Amsterdam University Press via ARPHA Platform.

Heritage, Memory and Conflict Journal is a brand new journal launched to trace back the remnants of the past – be it physical or anecdotal – back to their roots in the days of old. How do memory sites and discourses operate as vehicles at local, national and transnational levels and what indeed is the ‘cargo’ they carry? This is the type of questions authors from across disciplines – academic, artistic and industrial – will be trying to answer when preparing their manuscripts for HMC. 

Journal of European Landscapes (JEL) 

Homepage of the new Journal of European Landscapes published by Amsterdam University Press via ARPHA Platform.

Similarly, the second newly launched Journal of European Landscapes is to turn to history and cultural heritage, in order to understand the present use of the past when it comes to landscape. JEL’s founders point out that while Europe’s landscapes have so far enjoyed quite a lot of scientific attention, there isn’t a journal to address its indisputable and critical connection to heritage, even though the latter is what connects historical research with modern planning and management.

Vegetation Classification and Survey (VCS)

Homepage of the new Vegetation Classification and Survey journal published by the International Association for Vegetation Science via ARPHA Platform.

Adding up to the landscape topic is the Vegetation Classification and Survey (VCS) journal. This is the latest outlet launched by the International Association for Vegetation Science (IAVS): a worldwide union of scientists and other aficionados of theory and practice concerning the study of vegetation. 

With its transfer to ARPHA, VCS fulfils the mission of the union to move to Open Access. Interestingly, the journal supports two permanent sections: Ecoinformatics and Phytosociological Nomenclature. There, authors can submit certain unique article types: Review and Synthesis and Short/Long Database Reports. 

Devoted to plant community ecology, VCS publishes original research that works toward the development of novel vegetation classifications, as well as applied studies that use such typologies. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping. 

Plant Sociology 

Homepage of the new Plant Sociology journal published by Società Italiana di Scienza della Vegetazione via ARPHA Platform.

Another modern botany journal still awaiting its first issue since its transfer to ARPHA, is Plant Sociology, brought to life by the “Società Italiana di Scienza della Vegetazione” (SISV) with the aim to succeed the historical journals of the society: Fitosociologia (1990-2011) and Notiziario della Società Italiana di Fitosociologia (1964-1989).

The editorial management opted to have the journal co-published with Pensoft: the academic publisher and technology provider standing behind ARPHA. Thus, by default, the journal receives some extra perks as a result of Pensoft’s partnerships with leading innovators in the scholarly communication domain.  An excellent example would be the indexing and addition of each Plant Sociology article by the research discovery platform ScienceOpen in the “Pensoft Biodiversity” collection, following a recent strategic collaboration between the two Open Science champions.

With a wide scope covering vegetation studies from plant community to landscape level, Plant Sociology puts a special focus on topics such as plant sociology and vegetation survey for developing ecological models, as well as plant classification, monitoring, assessment, management and conservation, as long as the studies are based on rigorous and quantitative measures of physical and biological components.

Caucasiana

Adding up to the well-pronounced biodiversity theme in ARPHA’s and Pensoft’s journal portfolios, as well as the “Pensoft Biodiversity” collection on ScienceOpen, is the first Georgian journal to join the lines of the publishing platform. Caucasiana is to be co-published by the top biodiversity research centre in the region: Ilia State University in Tbilisi and Pensoft.

The scholarly outlet that we’ll soon see on ARPHA Platform is in fact a successor of an earlier journal launched by the Institute of Zoology of the Georgian Academy of Science that has been revamped top-to-bottom. Transformed into a technologically advanced publishing venue, Caucasiana’s task is to handle the growing research interest in the incredible, yet surprisingly overlooked animal, plant and fungal life of Caucasus and adjacent regions. 

Research published in Caucasiana will be well-positioned to bring this hotspot of biodiversity and endemism into focus for the global conservation movement.

The EASE Journal: European Science Editing (ESE)

The quarterly journal of the European Association of Science Editors (EASE): European Science Editing (ESE) is a key news source for all actors involved in scholarly publishing.

For the first time, ESE will open up its content to the public from day one of its publication, thanks to its move to ARPHA. While digital and print subscriptions used to be included as part of the association’s membership packages, other readers would have had to wait six months after print publication to receive free access.

Launched in 2003, ESE’s aim has been to keep editors posted about everything they need to know concerning scholarly communication. To do so, the journal publishes research articles, meeting reports, essays and viewpoints, as well as book and website reviews. Especially for members of the association, ESE takes care to highlight upcoming events and provide resources and publications, considered to be of their interest. 

Bulgarian Journal of Cardiology

In 2020, ARPHA will also welcome the third Bulgarian-born academic journal and the fourth covering the field of Medical Sciences to its open-access portfolio: the journal of Bulgaria’s National Cardiac Society, which is part of the European Society of Cardiology (ESC).

For the first time, the Bulgarian Journal of Cardiology will make use of the soon-to-be-released English-Bulgarian bilingual publishing solution from ARPHA. Similarly to the English-Russian approach to journal publishing, which was presented in Moscow in early December, ARPHA will allow for users of the Bulgarian Journal of Cardiology to not only publish papers in both English and Bulgarian, but also enjoy a top-to-bottom Bulgarian user interface.

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Learn more about ARPHA’s key features and achievements from 2019 in our yearly recap.

Experiment suggests the best ways to tackle invasive Oregon grape in Belgian coastal dunes

The Belgian coastal dunes, a protected habitat of high conservation value, are getting severely impacted by one of its worst enemies amongst invasive species: the Oregon grape. To help mitigate the detrimental effect of this North American shrub invader, Belgian scientists carried out an experiment to assess the effectiveness of different management methods.

The Belgian coastal dunes, a protected habitat of high conservation value, are getting severely impacted by one of its worst enemies amongst invasive species: the Oregon grape. To help mitigate the detrimental effect of this North American shrub invader, Belgian scientists carried out an experiment to assess the effectiveness of different management methods.

The Atlantic coastal dunes form a dynamic and diverse ecosystem, home to a large number of native species, many of which are regionally threatened. Embryonic dunes, shifting white dunes, moss dunes, dune grasslands, and dune slacks are considered high conservation value sites, according to the interpretation manual of European habitats. However, the dunes are highly affected by external influences, and one of the most important threats to their biodiversity are invasive non-native plant species. These plants often colonised the dunes as garden escapes or spread from garden waste dumps or public plantings. Oregon grape is one of the worst invaders amongst them.

Oregon grape growing on sand dune (Belgium).
Photo by Tim Adriaens.

In their study, published in the open-access journal NeoBiota, the scientists, led by Tim Adriaens and Sam Provoost of the Research Institute for Nature and Forest (INBO), focus on the management of the current populations of Oregon grape (Berberis aquifolium) in the Belgian coastal dunes, where the species has already managed to invade half of the 46 nature reserves and is starting to replace native vegetation. Such a negative effect on the biodiversity of the area requires practical management advice. Due to the high level of infestation of the dunes, the researchers recommend prompt eradication as the most appropriate management strategy. So far, however, it has been unclear which method would show the best effectiveness.

“Invasive shrub species exert an additional pressure on Belgian dune ecosystems, which are already highly fragmented by urbanisation. Oregon grape is one of the worst and should be tackled urgently before it gets out of control,” says Tim Adriaens.

Having compared four previously suggested treatments: manual uprooting, foliar herbicide application, stem cutting followed by herbicide and salt application, the scientists reported herbicide leaf treatment to be the most effective method. Manual removal by digging and treating stems with glyphosate showed medium effectiveness. Treating stems with a saturated salt solution appeared rather cosmetic. However, it’s not that easy to choose which method would be the best to work with, since with herbicide use there are non-target effects on the environment, economy, and society to be considered.

Dune restoration by mechanical removal of dense Oregon grape infestation (left) and leaf treatment of Oregon grape clone with a hand sprayer (right).
Photo by Tim Adriaens.

“Individual clones are best treated with herbicide, large surface areas provide opportunities for landscape-scale ecological restoration, combining invasive shrub removal with sand dune creation,” further explains Tim Adriaens.

In Belgium, Oregon grape was first recorded in the wild in 1906 and naturalised in the period 1920-1950. It has been spreading rapidly since the 1990s. This expansion might be linked to cultivated hybrids and global warming, with the latter leading to a lengthened growing season, suggest the scientists. The species likes calcareous soils. Along the Belgian coast, Oregon grape has mainly invaded grey dunes, scrub and woodland.

Thanks to its numerous blue berries, which are easily dispersed over long distances by songbirds, the plant can appear everywhere within the dunes sites, also in places hardly accessible to managers. With the help of a highly branched root system, the plants attach themselves firmly in the sand, which makes manual pulling of mature plants hardly possible and labor-intensive.

“Dune managers and scientists across Europe should unite to draft alert lists and prioritise established alien species for management,” Tim says in conclusion.

In conclusion, the scientists highlight the importance of an EU-wide collaboration between scientific communities. Invasive species are not bothered by administrative borders and exchanging experiences on impact and management options is crucial to maintain dune ecosystems in good conservation status.

Coastal dunes in Belgium provide unique habitat to many Red listed species.
Photo by Tim Adriaens.

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Original source

Adriaens T, Verschelde P, Cartuyvels E, D’hondt B, Vercruysse E, van Gompel W, Dewulf E, Provoost S (2019) A preliminary field trial to compare control techniques for invasive Berberis aquifolium in Belgian coastal dunes. NeoBiota 53: 41-60. https://doi.org/10.3897/neobiota.53.38183

Strategic collaboration agreement signed between ScienceOpen and Pensoft

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination.

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration partnership with the aim of strengthening the companies’ identities as the leaders of innovative content dissemination. The new cooperation will focus on the unified indexation, the integration of Pensoft’s ARPHA Platform content into ScienceOpen and the utilization of novel streams of scientific communication for the published materials.

Pensoft is an independent academic publishing company, well known worldwide for bringing novelty through its cutting-edge publishing tools and for its commitment to open access practices. In 2013, Pensoft launched the first ever, end-to-end, XML-based, authoring, reviewing and publishing workflow, now upgraded to the ARPHA Publishing Platform. As of today, ARPHA hosts over 50 open access, peer-reviewed scholarly journals: the whole Pensoft portfolio in addition to titles owned by learned societies, university presses and research institutions.

As part of the strategic collaboration, all Pensoft content and journals hosted on ARPHA are indexed in the ScienceOpen’s research and discovery environment, which puts them into thematic context of over 60 million articles and books. In addition, thousands of articles across more than 20 journals were integrated into a “Pensoft Biodiversity” Collection. Combined this way, the content benefits from the special infrastructure of ScienceOpen Collections, which supports thematic groups of articles and books equipped with a unique landing page, a built-in search engine and an overview of the featured content. The Collections can be reviewed, recommended and shared by users, which facilitates academic debate and increases the discoverability of the research.

The Pensoft Biodiversity collection is available from: https://www.scienceopen.com/collection/PensoftBiodiversity

“It is certainly great news and a much-anticipated milestone for Pensoft, ARPHA and our long-year partners and supporters from ScienceOpen to have brought our collaboration to a new level by indexing the whole ARPHA-hosted content at ScienceOpen,” comments Pensoft’s and ARPHA’s CEO and founder Prof. Lyubomir Penev. “Most of all, the integration between ARPHA and ScienceOpen at an infrastructural level means that we will be able to offer this incredible service and increased visibility to newcoming journals right away. On the other hand, by streaming fresh and valuable publicly accessible content to the ScienceOpen database, these journals will be further adding to the growth of science in the open.”

Stephanie Dawson, CEO of ScienceOpen says, “I am particularly excited to add new high-quality, open access biodiversity content from Pensoft Publishers to the ScienceOpen discovery environment as we have a very active community of researchers on ScienceOpen creating and sharing Collections in this field. We are looking forward to working with Pensoft’s innovative journals to support their open science goals.”

The collaboration reflects not only the commitment of both Pensoft and ScienceOpen to new methods of knowledge dissemination, but also the joint mission to champion open science through innovation. The two companies will cooperate at a strategic level in order to increase the international outreach of their content and services, and to make them even more accessible to the broad community.

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About ScienceOpen:

From promotional collections to Open Access hosting and full publishing packages, ScienceOpen provides next-generation services to academic publishers embedded in an interactive discovery platform. ScienceOpen was founded in 2013 in Berlin and Boston by Alexander Grossmann and Tibor Tscheke to accelerate research communication.

Unlikely wasp enemy of a serious alien pest in North America named Idris elba

A new species of wasp discovered in Mexico and named Idris elba, could help in managing the serious non-native bagrada bug, which already damages vegetable crops across North America.

While a mention of the British movie and music star is missing in its description, the species might prove to be a Heimdall-like ‘protector’ for many crops

A parasitic wasp was recently discovered in Guanajuato, Mexico, where it was found to parasitize the eggs of an invasive stink bug, known as the bagrada bug, which is a major pest of cruciferous vegetables. A research team from Colegio de Postgraduados (Mexico), Agriculture and Agri-Food Canada (AAFC) and the Florida State Collection of Arthropods (FSCA) collaborated to publish a study on the biology this species, Idris elba, and describe it as a species new to science.

The genus Idris was described in 1856 and now contains over 300 species and many more species are still undescribed. Species of Idris were previously known to only parasitize spider eggs. It was thus very unexpected when specimens of Idris were found to emerge from eggs of the bagrada bug by Dr. Refugio Lomeli-Flores and his team in Guanajuato. Advanced methods in molecular forensics were used by Dr. Tara Gariepy (AAFC) to match the DNA of the adult wasp with DNA left behind in the stink bug egg from which it emerged, independently confirming the results. The specimens were then sent to taxonomist, Dr. Elijah Talamas (FSCA), who determined that it was an undescribed species.

The discovery of this wasp marks an important step toward the development of efficient and natural control of the stink bug species Bagrada hilaris in North America. Commonly known as the bagrada bug, it is native to Africa, but is already an established and important pest of over 74 plant species in India, southern Europe, southern Asia and the Middle East.

Аcross the Atlantic, it has been known since 2008, when it was reported from Los Angeles, California (USA), followed by records from Coahuila state, Mexico, in 2014. Three years later, it was also found in the state of Guanajuato, which is responsible for over 70% of the country’s broccoli production, as well as the major import of broccoli and cauliflower in the USA and Canada. So far, measures to halt the bug’s invasion have proven largely ineffective, and its distribution is expected to reach new ecosystems of economical importance.

Non-parasitized (left) compared with a parasitized (right) bagrada bug egg, where an
Idris elba wasp was observed to emerge.
Image by Elijah J. Talamas

While not unheard of, it is uncommon for native parasitoids to attack an introduced host. Idris elba is exceptional because it demonstrates that these wasps can make the leap from parasitizing the eggs of spiders to the eggs of stink bugs. Having rejected the possibility of the species having been introduced alongside its host, the scientists note that the unexpected association could be either the result of a broad host range, or a case of lucky confusion, where the parasitoid tends to mistake the eggs of the stink bug for those of a spider.

It is no coincidence that this wasp has the species name “elba”. Dr. Talamas explained that explicitly naming the species after Idris Elba (the actor), also known as a patronym, would have to follow Latin grammar and become Idris elbai. By treating the second name as an arbitrary combination of letters, the grammar was avoided.

Four-time Golden Globe nominee for Best Actor, Idris Elba is a famous British actor, producer, writer, singer, DJ and producer, best known for a long list of blockbusters, including a good number of superhero movies, such as the Marvel series inspired by the myths of the Norse god Thor. There, Elba stars as Heimdall, whose almost namesake: Heimdallr, is a Norse deity believed to be the sole protector of the bridge linking the human world and the realm of the gods.

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Original source:

Lomeli-Flores JR, Rodríguez-Rodríguez SE, Rodríguez-Levya E, González-Hernández H, Gariepy TD, Talamas EJ (2019) Field studies and molecular forensics identify a new association: Idris elba (Talamas), sp. nov. parasitizes the eggs of Bagrada hilaris (Burmeister). In: Talamas E (Eds) Advances in the Systematics of Platygastroidea II. Journal of Hymenoptera Research 73: 125-141. https://doi.org/10.3897/jhr.73.38025

Stuck in a Polish nuclear weapons bunker cannibal wood ants find the way home

In a recent development of the story about wood ants trapped in a post-Soviet nuclear weapons bunker in Poland, scientists, led by Prof. Wojciech Czechowski, with the decisive contribution of Dr. István Maák, both from the Museum and Institute of Zoology, Polish Academy of Sciences in Warsaw, deduced that the “colony” (in quotation marks because only workers were found), while lacking other food, had to survive on the corpses of imprisoned nestmates. By using an experimentally installed boardwalk, the ants were helped to get through the ventilation pipe that led out of the bunker and back to their maternal nest on the top.

The ants were discovered in 2013 thanks to a yearly campaign set to count hibernating bats in the same bunker. The scientific report was published in 2016 also in Journal of Hymenoptera Research. At that time, the scientists estimated the presence of at least several hundred thousand workers, arguably close to a million. The insects ended up in this situation as a result of large numbers of wood ants continuously falling down a ventilation pipe to never return to their nest on top of the bunker. Several years later, the “colony” still appeared to be thriving, despite being trapped in a confined space with no light, heat and obvious source of food.

In the newly published paper, the scientists sought out whether while lacking alternative food, the wood ants would consume the dead bodies of their conspecifics that were accumulating on the bunker floor. In nature, a similar behaviour occurs frequently during spring, when protein food is scarce. These are the so-called “ant wars”, which serve to set the boundaries of the territories of neighbouring conspecific colonies of wood ants, while simultaneously providing food in the form of the fresh corpses of the numerous victims.

Recent research has also shown that corpse consumption in wood ants is more common than it was previously thought, and that nestmate’s corpses can serve as an important food source not only in periods of food shortage.

Taking into account the clear signs of cannibalism in the bunker with practically no other organisms to feed on the ant cadavers, the scientists could safely deduce that the bunker “colony” survived indeed on consuming mostly dead nestmates.


“The present case adds a dimension to the great adaptive ability of ants to marginal habitats and suboptimal conditions, as the key to understanding their unquestionable eco-evolutionary success”, added the authors.


“

In the spring of 2016, the scientists decided to free the captive ants. At first, they released a group of one hundred ants from the bunker into the outskirts of the mother nest, in order to confirm the relation between the two partly isolated groups. As expected, no aggressive behaviour was observed. In September, a 3-metre-long vertical boardwalk with one end burrowed in the mound made by the bunker “colony” and the other one tucked inside the ventilation pipe was constructed. Soon, individual ants started to inspect the escape route. By February 2017, the nuclear weapon bunker was almost deserted. Meanwhile, the maternal wood ant colony still nests at the top of the bunker at the outlet of the ventilation pipe, and ants continue to fall down through the pipe. However, the boardwalk now allows them to move freely up and down.


“So, we can expect further intriguing ant behaviour,” comment the scientists.

Research article:

Rutkowski T, Maák I, Vepsäläinen K, Trigos-Peral G, Stephan W, Wojtaszyn G, Czechowski W (2019) Ants trapped for years in an old bunker; survival by cannibalism and eventual escape. Journal of Hymenoptera Research 72: 177-184. https://doi.org/10.3897/jhr.72.38972

Facebook and Instagram gave away the presence of the ‘Japan pig’ seahorse in Taiwan

Japan pig seahorse (Hippocampus japapigu) in its natural habitat at Hejie, Kenting, Taiwan

Credit: Chao-Tsung Chen
License: CC-BY 4.0

While monitoring of cryptic and elusive tiny creatures, such as pygmy seahorses that measure only 13 to 27 mm, might be too costly and time-consuming for research teams and institutions, the underwater activity might be proving of particular interest to photography and diving enthusiasts.

At least, this is what comes across from the recent reports of five miniature species identified from Taiwanese waters by local citizen scientists and passed along via Facebook and Instagram. Amongst the findings, there are two species that had never before been reported from the country, including last year’s media sensation: the ‘Japan pig’, considered to only be found in the “Land of the Rising Sun”. The study, conducted by the team Mr. Joseph Heard,  Drs Jeng-Ping Chen and Colin Wen from Tunghai University and Taiwan Ocean Research Institute, is published in ZooKeys, the very same open-access journal that saw the description of the species in 2018.

The scientists note that pygmy seahorses are largely unknown species and even basic information regarding their habitats is largely inconsistent and based on unofficial reports. As monitoring of marine wildlife can be expensive and time-consuming, especially regarding its small and cryptic representatives, the researchers decided to use “Phone a Friend” lifeline. Scuba divers and underwater photographers were approached on social media to help investigate pygmy seahorse diversity in Taiwan.

Their call resulted in 259 social media items, including 75 photos of 78 miniature creatures from their natural habitats at five different locations. Identified as five separate species, their discovery ranks Taiwan as one of the world’s biodiversity hotspots for pygmy seahorse, given that there are only seven species of pygmy seahorses out there.

A Japan pig seahorse (Hippocampus japapigu) in its natural habitat at Green Island, Taiwan.
Credit: Jolly Huang
License: CC-BY 4.0

Four of those were found at Green Island alone, a small volcanic Pacific island, measuring only 15 km2. 

Pygmy seahorse specimen collection from Taiwan for future examination is still undergoing.

Heard J, Chen J-P, Wen CKC (2019) Citizen science yields first records of Hippocampus japapigu and Hippocampus denise (Syngnathidae) from Taiwan: A hotspot for pygmy seahorse diversity. ZooKeys 883: 83-90. https://doi.org/10.3897/zookeys.883.39662 

Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlazi, Pensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

Prof. Lyubomir Penev, founder and CEO of Pensoft says,

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”

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Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

Could biodiversity data be finally here to last?

While digital curation, publication and dissemination of data have been steadily picking up in recent years in scientific fields ranging from biodiversity and ecology to chemistry and aeronautics, so have imminent concerns about their quality, availability and reusability. What’s the use of any dataset if it isn’t FAIR (i.e. findable, accessible, interoperable and reusable)?  

With the all-too-fresh memory of researchers like Elizabeth “Lizzie” Wolkovich who would spend a great deal of time chasing down crucial and impossible-to-replicate data by means of pleading to colleagues (or their successors) via inactive email addresses and literally dusting off card folders and floppy disks, it is easy to imagine that we could be bound to witness history repeating itself once more. At the end of yet another day in today’s “Big Data” world, data loss caused by accidental entry errors or misused data standards seems even more plausible than an outdated contact or a drawer that has suddenly caught fire. 

When a 2013 study, which looked into 516 papers from 1991 to 2011, reported that the chances of associated datasets to be available for reuse fell by 17% each year starting from the publication date, it cited issues mostly dealing with the data having simply been lost through the years or stored on currently inaccessible storage media. However, the researcher of today is increasingly logging their data into external repositories, where datasets are swiftly provided with a persistent link via a unique digital object identifier (DOI), while more and more publishers and funders require from authors and project investigators to make their research data openly available upon the publication of the associated paper. Further, we saw the emergence of the Data Paper, a research article type later customised for the needs of various fields, including biodiversity, launched in order to describe datasets and facilitate their reach to a wider audience. So, aren’t data finally here to last? 

The majority of research funders, such as the EU’s Framework Programme Horizon2020, have already adopted Open Access policies and are currently working on their further development and exhaustiveness.

Credit: OpenAIRE Research Data Management Briefing paper, available to download from <https://www.openaire.eu/briefpaper-rdm-infonoads/download>.

Today, biodiversity scientists publish and deposit biodiversity data at an unprecedented rate and the pace is only increasing, boosted by the harrowing effects of climate change, species loss, pollution and habitat degradation among others. Meanwhile, the field is yet to adopt universal practices and standards for efficiently linking all those data together – currently available from rather isolated platforms – so that researchers can indeed navigate through the available knowledge and build on it, rather than duplicate unknowingly the efforts of multiple teams from across the globe. Given the limited human capabilities as opposed to the unrestricted amounts of data piling up by the minute, biodiversity science is bound to stagnate if researchers don’t hand over the “data chase” to their computers.

Truth be told, a machine that stumbles across ‘messy’ data – i.e. data whose format and structure have been compromised, so that the dataset is no longer interoperable, i.e. it fails to be retrieved from one application to another – differs little from a researcher whose personal request to a colleague is being ignored. Easily missable details such as line breaks within data items, invalid characters or empty fields could lead to data loss, eventually compromising future research that would otherwise build on those same records. Unfortunately, institutionally available data collections are just as prone to ‘messiness’, as evidenced by data expert and auditor Dr Robert Mesibov. 

“Proofreading data takes at least as much time and skill as proofreading text,” says Dr Mesibov. “Just as with text, mistakes easily creep into data files, and the bigger the data file, the more likely it has duplicates, disagreements between data fields, misplaced and truncated (cut-off) data items, and an assortment of formatting errors.”

Snapshot from a data audit report received by University of Cordoba’s Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa while preparing their data paper, which describes the herbarium dataset for the vascular plants in COFC.

Similarly to research findings and conclusions which cannot be considered truthful until backed up by substantial evidence, the same evidence (i.e. a dataset) should be of questionable relevance and credibility if its components are not easily retrievable for anyone wishing to follow them up, be it a human researcher or a machine. In order to ensure that their research contribution is made in a responsible fashion in compliance with good scientific practices, scientists should not only care to make their datasets openly available online, but also ensure they are clean and tidy, therefore truly FAIR. 

With the kind help of Dr Robert Mesibov, Pensoft has implemented mandatory data audit for all data paper manuscripts submitted to the relevant journals in its exclusively open access portfolio to support responsibility, efficiency and FAIRness in biodiversity science. Learn more about the workflow here. The workflow is illustrated in a case study, describing the experience of University of Cordoba’s Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa, while preparing their data paper later published in PhytoKeys. A “Data Quality Checklist and Recommendations” is accessible on the websites of the relevant Pensoft journals, including Biodiversity Data Journal.

CASE STUDY: Data audit for the “Vascular plants dataset of the COFC herbarium (University of Cordoba, Spain)”, a data paper in PhytoKeys

Following the submission of their data paper manuscript, which serves to describe the herbarium dataset of vascular plants at the University of Cordoba (Spain), to the open access journal PhytoKeys, Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa received a data audit report, prepared by data specialist Dr Robert Mesibov. 

The dataset described in Dr Gloria Martínez-Sagarra’s and Prof Juan Antonio Devesa’s paper is registered and available from the GBIF portal.



As part of the routine workflow, which is mandatory for data papers submitted across relevant Pensoft journals, their work underwent a technical evaluation against a checklist of data quality features, compiled in such a fashion that it ensures uncompromised accessibility, readability and interoperability of the data, regardless of whether its next user is a human or a machine. 

To do so, it is crucial that any issues concerning the data structure and format within a dataset – which could potentially cause data loss down the line – need to be identified and addressed prior to the publication of the data paper, in fact, before it is even assigned to a subject editor. Only after the data audit is performed, can a manuscript proceed to peer review. In case there are major issues with the dataset, the data paper can be rejected right away, but resubmitted after the necessary corrections are applied.

In the report, the authors could find a list of identified issues as well as recommendations from Dr Mesibov. Similarly to a conventional peer review, these comments are meant to pinpoint any areas that need to be corrected straight away, as well as those that might only need a bit of further clarification. After receiving the data audit report, the authors take their turn to address the feedback.

Snapshot from the data auditing report received by Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa for their data paper manuscript submitted to PhytoKeys.

In the present case, the report features a list of discrepancies between the counts of taxonomic records as listed in the data paper as opposed to those in the original dataset, i.e. verbatim.txt. Here, as it turned out, the disagreement is due to various taxonomic revisions that have taken place within the highlighted families since the dataset’s last update on GBIF.

Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa sent back their comments on the issues addressed in the data audit report.

In other cases, however, data entry errors, such as inappropriately used fields and  non-compliance with the Darwin Core recommendations, had to be cleaned, in order to prevent data loss and compromised interoperability.

With the problematic data corrected, the manuscript proceeded to peer review and was accepted for publication five days later.

Editor’s user interface on the PhytoKeys website showing the progress of the manuscript from submission to acceptance.

Having followed the strong recommendations from Pensoft, the authors also re-uploaded their revised data to GBIF.

Data audit workflow provided for data papers submitted to Pensoft journals.

As a result, both the data paper and the associated dataset are not only published in an open access, peer-reviewed journal and safely stored at GBIF, but also verified as Findable, Accessible, Interoperable and Reusable. 

Thanks to the thorough work and additional efforts of University of Cordoba’s Dr Gloria Martínez-Sagarra and Prof Juan Antonio Devesa, future researchers working on the Andalusian flora can already rely on a real head start.

Find more about the Pensoft’s mandatory data quality workflow in this blog post.