Tag: Pensoft

Research on bats and pangolins – potential vectors of zoonotic pandemics like COVID-19 – invited to a free-to-publish special issue in ZooKeys

Captively bred pangolins. 
Photo by Hua L. et al., taken from their study on the current status, problems and future prospects of captive breeding of pangolins, openly accessible in ZooKeys at: https://doi.org/10.3897/zookeys.507.6970

Accepted papers will be published free of charge in recognition of the emergency of the current global situation

Was it the horseshoe bat or could it rather be one of the most traded mammal in the world: the pangolin, at the root of the current devastating pandemic that followed the transmission of the zoonotic SARS-CoV-2 virus to a human host, arguably after infected animal products reached poorly regulated wet markets in Wuhan, China, last year? 

To make matters worse, the current situation is no precedent. Looking at the not so distant past, we notice that humanity has been repeatedly falling victim to viral deadly outbreaks, including Zika, Ebola, the Swine flu, the Spanish flu and the Plague, where all are linked to an animal host that at one point, under specific circumstances transferred the virus to people. 

Either way, here’s a lesson humanity gets to learn once again: getting too close to wildlife is capable of opening the gates to global disasters with horrific and irreversible damage on human lives, economics and ecosystems. What is left for us to understand is how exactly these transmission pathways look like and what are the factors making certain organisms like the bat and the pangolin particularly efficient vectors of diseases such as COVID-19 (Coronavirus). This crucial knowledge could’ve been easier for us to grasp had we only obtained the needed details about those species on time.

Aligning with the efforts of the biodiversity community, such as the recently announced DiSSCo and CETAF COVID-19 Task Force, who intend to create an efficient network of taxonomists, collection curators and other experts from around the globe and equip them with the tools and large datasets needed to combat the unceasing pandemic, the open-access peer-reviewed scholarly journal ZooKeys invites researchers from across the globe to submit their work on the biology of bats and pangolins to a free-to-publish special issue. 

The effort will be coordinated with the literature digitisation provider Plazi, who will extract and liberate data on potential hosts from various journals and publishers. In this way, these otherwise hardly accessible data will be re-used to support researchers in generation of new hypotheses and knowledge on this urgent topic.

By providing further knowledge on these sources and vectors of zoonotic diseases, this collection of publications could contribute with priceless insights to make the world better prepared for epidemics like the Coronavirus and even prevent such from happening in the future. 

Furthermore, by means of its technologically advanced infrastructure and services, including expedite peer review and publication processes, in addition to a long list of indexers and databases where publications are registered, ZooKeys will ensure the rapid publication of those crucial findings, and will also take care that once they get online, they will immediately become easy to discover, cite and built on by any researcher, anywhere in the world. 

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The upcoming “Biology of bats and pangolins” special issue is to add up to some excellent examples of previous research on the systematics, biology and distribution of pangolins and bats published in ZooKeys. 

In their review paper from 2015, Chinese scientists looked into the issues and prospects around captive breeding of pangolins. A year later, their colleagues at South China Normal University provided further insights into captive breeding, in addition to new data on the reproductive parameters of Chinese pangolins.

Back in 2013, a Micronesian-US research studied the taxonomy, distribution and natural history of flying fox bats inhabiting the Caroline Islands (Micronesia). A 2018 joint study on bat diversity in Sri Lanka focused on chiropteran conservation and management; while a more recent article on the cryptic diversity and range extension of the big-eyed bats in the genus Chiroderma. 

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For more information, visit ZooKeys website. 

Follow ZooKeys on Twitter and Facebook.

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References:

Buden D, Helgen K, Wiles G (2013) Taxonomy, distribution, and natural history of flying foxes (Chiroptera, Pteropodidae) in the Mortlock Islands and Chuuk State, Caroline Islands. ZooKeys 345: 97-135. https://doi.org/10.3897/zookeys.345.5840

Edirisinghe G, Surasinghe T, Gabadage D, Botejue M, Perera K, Madawala M, Weerakoon D, Karunarathna S (2018) Chiropteran diversity in the peripheral areas of the Maduru-Oya National Park in Sri Lanka: insights for conservation and management. ZooKeys 784: 139-162. https://doi.org/10.3897/zookeys.784.25562

Hua L, Gong S, Wang F, Li W, Ge Y, Li X, Hou F (2015) Captive breeding of pangolins: current status, problems and future prospects. ZooKeys 507: 99-114. https://doi.org/10.3897/zookeys.507.6970

Lim BK, Loureiro LO, Garbino GST (2020) Cryptic diversity and range extension in the big-eyed bat genus Chiroderma (Chiroptera, Phyllostomidae). ZooKeys 918: 41-63. https://doi.org/10.3897/zookeys.918.48786

Zhang F, Wu S, Zou C, Wang Q, Li S, Sun R (2016) A note on captive breeding and reproductive parameters of the Chinese pangolin, Manis pentadactyla Linnaeus, 1758. ZooKeys 618: 129-144. https://doi.org/10.3897/zookeys.618.8886

Vegetation Classification and Survey (VCS), the new journal of the Int’l Association for Vegetation Science

The journal is to launch with a big editorial and several diverse, high-quality papers over the next months

In summer 2019 IAVS decided to start a new, third association-owned journal, Vegetation Classification and Survey (VCS), next to Journal of Vegetation Science (JVS) and Applied Vegetation Science (AVS).

Vegetation Classification and Survey (VCS) is an international, peer-reviewed journal of plant community ecology published on behalf of the International Association for Vegetation Science (IAVS) together with its sister journals, Journal of Vegetation Science (JVS) and Applied Vegetation Science (AVS). It is devoted to vegetation survey and classification at any organizational and spatial scale and without restriction to certain methodological approaches.

The journal publishes original papers that develop new vegetation typologies as well as applied studies that use such typologies, for example, in vegetation mapping, ecosystem modelling, nature conservation, land use management or monitoring. Particularly encouraged are methodological studies that design and compare tools for vegetation classification and mapping, such as algorithms, databases and nomenclatural principles. Papers dealing with conceptual and theoretical bases of vegetation survey and classification are also welcome. While large-scale studies are preferred, regional studies will be considered when filling important knowledge gaps or presenting new methods. VCS also contains Permanent Collections on “Ecoinformatics” and “Phytosociological Nomenclature”.

VCS is published by the innovative publisher Pensoft as a gold open access journal. Thanks to support from IAVS, we can offer particularly attractive article processing charges (APCs) for submissions during the first two years. Moreover, there are significant reductions for IAVS members, members of the Editorial Team and authors from low-income countries or with other financial constraints (learn more about APCs here).

Article submissions are welcomed at: https://vcs.pensoft.net/

Post by Jürgen Dengler, Idoia Biurrun, Florian Jansen & Wolfgang Willner, originally published on Vegetation Science Blog: Official blog ot the IAVS journals.

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Follow Vegetation Classification and Survey on Twitter and Facebook.

Food Modelling Journal: New open-access venue provides a platform for food scientists

The open-access Food Modelling Journal (FMJ) was launched by the AGINFRA+ community and Pensoft with the aim to encourage food science specialists, agronomists and computer scientists to come together and work on assuring and improving food supply, quality and safety in our globalised and rapidly changing world.

An introductory editorial and an article of a unique publication type are already made available in the next-generation journal

The open-access Food Modelling Journal (FMJ) was launched by the AGINFRA+ community and Pensoft with the aim to encourage food science specialists, agronomists and computer scientists to come together and work on assuring and improving food supply, quality and safety in our globalised and rapidly changing world.

The Food Modelling Journal will be focusing on the publication of information objects and digital resources in the food science field, related (but not limited) to: food safety, food quality, food control, food defence and food design, documenting experimental or observational data and mathematical models.

By providing a platform and tools for describing scientific records and crediting for dedicated models, data, data analytics workflows and software, FMJ fosters the overall reproducibility and reusability of research.

FMJ also aims to shed light on what we refer to as research objects – data, software scripts, visualisation routines or models. Usually, they would stay undervalued, underused and uncredited, despite their importance for the scientific progress.

The focus and scope of the journal are supported by a number of specific key features:

  • Quality but not quantity
  • Cross-disciplinary approach
  • Open data and software code policy
  • Rapid turnaround time
  • Advanced open access and machine-readability.

It should be noted that the Open Science movement and the barrier-free access to research, is at the heart of the FMJ project.

To support its authors, the AGINFRA+ community, Pensoft and Food Modelling Journal have provided them access to the ARPHA Writing Tool, where researchers are able to work together with their co-authors, colleagues and peers on manuscripts from the drafting stage to publication.

A FSKX model run using the executable paper feature available in Food Modelling Journal.

A particularly appealing feature, meant to promote reproducibility, collaboration and openness in science, is the executable papers, where users can reproduce research findings using the published model and running it either with default or new parameters. By clicking an “Execute” button within the body of the article, users are taken to an external virtual environment where they will be able to execute the computation. By ‘encapsulating’ all the details needed to perform the action within the paper, this feature ensures that the published findings will remain testifiable in the future.

“While the long-lasting tradition in science used to focus on crediting researchers’ work through conventional research articles and especially by counting their citations, many exciting, useful and often invaluable products of the research cycle, such as data, software scripts, visualisation routines or models (usually called “research objects”) normally stay undervalued, underused and uncredited, despite their importance for scientific progress,” note the editorial board in the introductory editorial.

“The consequences of this neglect of the initial and intermediate steps of the research cycle in favour of the research articles or research books are obvious: scientists often repeat efforts done by others instead of using these as a stepping stone for further analyses and generating new knowledge, let alone the impossible or restricted reproducibility and reusability of research results,” they add.

The first paper of a unique publication type: FSKX (Food Safety Knowledge), is already publicly accessible in the journal. Classified as an early research outcome, the article presents a new generic model for assessing the risk of salmonellosis associated with the consumption of table eggs. To ensure the reusability of the model, the research team of Virginie Desvignes (ANSES – French Food Safety Agency) have made it available in the Food Safety Knowledge Markup Language (FSK-ML) format alongside the executable model script, visualisation script and simulation settings.

FSK-ML is an open information exchange format that is based on harmonised terms, metadata and controlled vocabulary to harmonise annotations of risk assessment models and that was significantly improved and extended during the AGINFRA+ project.

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Follow Food Modelling Journal on Twitter and Facebook.

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Food Modelling Journal is indexed by BASE, CNKI, CrossRef, Dimensions, Google Scholar, J-Gate, Mendeley, Microsoft Academic, Naviga (Softweco), OCLC WorldCat, OpenAIRE, OpenCitations, ReadCube, Transpose, Ulrichsweb™ and Unpaywall; and archived at CLOCKSS, Zenodo and Portico.

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.

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.

All Pensoft journals indexed in Transpose to support transparency in journal policies

All open-access, peer-reviewed academic titles of Pensoft‘s, as well as those using the white-label publishing solution provided by the scholarly publishing platform ARPHA, have their journal policy data fed into the Transpose database, in order to increase their discoverability and transparency.

Thanks to the recent integration with the community-sourced initiative Transpose, details about each journal’s approach to peer review, co-review and preprint publication can be easily accessed, navigated and compared through a user-friendly interface. Visitors can also query the data by journal title, publisher, ISSN or DOI, and apply several filters.

Having estimated that almost 1/3 of the top-cited journals across disciplines do not provide clearly basic information about their editorial policies, including whether they operate blind peer review or not, the team behind Transpose launched the forward-thinking community-sourced initiative with the aim to advance practices in academia and increase awareness and transparency amongst authors, editors and many other stakeholder groups. To highlight the essentiality of free and easy access to editorial policies for a wide range of actors, Transpose have published user testimonials on their website coming from various points of view, including early researchers, supervisors, project investigators, funders, publishing staff, and others.


Recent integration of the scholarly publishing platform ARPHA and Transpose results in the editorial policies of all ARPHA-hosted journals being fed into the associated database. Thus, various stakeholders from across the academic landscape are provided with an easy access to details about the peer review, co-review and preprint policies at each journal via a user-friendly interface.

Pensoft and ARPHA’s founder and CEO Prof. Lyubomir Penev says:

“Having been Open Science advocates from the very beginning, at Pensoft and ARPHA, we have always supported our clients and users in being as transparent as possible. Favourite examples are the open-science journal Research Ideas and Outcomes (RIO), welcoming continuously updatable publications from across the whole research cycle, and Rethinking Ecology, launched to voice innovative and even bold ideas for the purposes of taking swift actions towards the conservation of the environment. The former operates public pre- and post-publication peer review to support efficient collaboration in research, while the latter relies on double-blind peer reviews, in order to encourage researchers of various experience and background to share their inventive ideas in ecology. Obviously, journal policies are and should be crucial when it comes to picking a specific journal over another regardless of the perspective. This is why I am certain that joining Transpose is doing good for all ARPHA-hosted journals, as well as the academic community.”

ASAPbio‘s Executive Director and member of the team behind Transpose, Dr Jessica Polka adds:

“We’re thrilled to incorporate data from Pensoft into Transpose. Making policy information clear and easy to find ensures that authors and reviewers can work with journals that best align with their values — and that scholarly work can be fairly interpreted by everyone, including general readers.”

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Additional information:

About Transpose:

Transpose is an initiative to build a database of journal policies. It focuses on three areas: open peer review, co-reviewing, and detailed pre-printing policies. It welcomes contributions from anyone, but seeks verification from journals and publishers. The goal of Transpose is to foster new practices while increasing awareness among authors, editors, and other stakeholders, and we seek to provide resources to assist journals in setting, sharing, and clarifying their policies.

Bulgarian Pharmaceutical Scientific Society’s journal moves to high-tech ARPHA platform

Bulgarian Pharmaceutical Scientific Society’s journal join the high-tech ARPHA platform and the fast-expanding portfolio of scholarly titles by Pensoft.Bulgarian Pharmaceutical Scientific Society’s journal join the high-tech ARPHA platform and the fast-expanding portfolio of scholarly titles by Pensoft.

The established Pharmacia demonstrates a complete makeover in its new issue after signing with scientific publisher and technology provider Pensoft and its signature open-access platform

Launched by the Bulgarian Pharmaceutical Scientific Society in 1954, the open-access, peer-reviewed Pharmacia has been available online as full text since 2007. As of 2019, the journal moves to the fast-expanding portfolio of scholarly publisher and technology provider Pensoft. The journal’s 2019 inaugural issue and the first since the realisation of the new partnership is already live on the journal’s new website.

Homepage of Pharmacia‘s new website, https://pharmacia.pensoft.net

Thanks to the Pensoft’s signature open-access scholarly publishing platform ARPHA, Pharmacia demonstrates a complete makeover, including a modern and user-friendly interface in addition to a long list of high-tech perks, meant to ensure that published articles are easy to discover, access, cite and reuse by both humans and machines all over the world.

Furthermore, all users of the journal’s system: authors, editors and reviewers alike, are to greatly benefit of ARPHA’s integrated approach to the publication process. This means that once submitted each manuscript goes through the whole cycle: from review and copy/layout editing to publication, dissemination and archiving without leaving ARPHA’s collaboration-focused online environment.

One of the interesting features now available in Pharmacia is the article-level metrics available thanks to the partnership between ARPHA and the revolutionary discovery and analytics tools Dimensions and Altmetric. By searching through millions of research articles, grant applications, clinical trials, as well as policy documents, news stories, blogs and social media posts, they allow for each article’s references and citations in both the academic and the public sphere to be monitored in real time.

Continuing its tradition, the journal welcomes original research and review articles, preliminary and short communications (notes) on a wide range of topics within the pharmaceutical and related sciences. In addition, the journal also publishes conference reports, biographies and book reviews. Articles in Pharmacia are published in English and subjected to single-blind peer review.

Pharmacia‘s Editor-in-Chief Prof Plamen Peikov, comments:

“We have been looking forward to our collaboration with Pensoft and ARPHA, as it is certainly going to not only help modernise Pharmacia on the outside, but also make it more appealing to our authors and readers by building on the journal’s accessibility and global outreach. I believe that this nice step forward is already clearly evident in Pharmacia‘s latest issue.”

ARPHA’s and Pensoft’s founder and CEO Prof Lyubomir Penev says:

“I’m delighted to see this particular journal joining the Pensoft’s and ARPHA’s family,” says ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev. “With our strong background in scholarly publishing, technology development and open science practices, I am certain that we are able to provide the right venue for a high-quality and enterprising journal like Pharmacia.”

What’s on in the new issue?

The creeping cinquefoil – a perennial plant from the Northern hemisphere – has its status as a traditional medicine for treating diarrhoea, haemorrhoids and bleeding gums confirmed in a collaborative ethnobotanical study by researchers at the Bulgarian Academy of Sciences and the Medical University of Sofia (Bulgaria). Further, the team, led by Irena Mincheva, seek to explore the suggested use of the plant against mastitis: a relatively common disease and a major cause for milk reduction in both people and dairy cows.

Another paper, authored by Dr Illya Podolsky and Sergiy Shtrygol from the National University of Pharmacy in Ukraine, adds new information about “the pharmacological nature” of a molecule already known as a promising antidepressant with a unique spectrum of additional properties. By conducting an experiment in rats, using the preferred Morris water maze assessment method, the scientists study the effects of Atristamine on spatial memory and learning.

Pharmacia‘s latest issue is available on the new website. Available in HTML, XML and PDF formats, the articles are easy to find, access, mine, reuse and cite by both humans and computers. Check out the issue at: https://pharmacia.pensoft.net/issue/1757/.

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Pharmacia is indexed byScopus, Altmetric, Biotechnobase, CAplusSM/Chemical Abstracts, CNKI, CrossRef, Dimensions, EBSCOhost, Embase, ExtraMED, Google Scholar, J-Gate, MEDLINE/PubMed, Mendeley, Microsoft Academic, Naviga (Softweco), OpenAIRE, Pascal, ReadCube, Toxcenter, Unpaywall.

About the Bulgarian Pharmaceutical Scientific Society:

The Bulgarian Pharmaceutical Scientific Society was registered in 2003 with the aim to organise national and international science forums, support education and publish academic literature. Its main objectives are to organise and encourage pharmacological research and support collaboration between pharmacology professionals and related organisations on both national and global level.

Austrian Herpetological Society’s journal Herpetozoa moves to Pensoft’s ARPHA platform

Newly published research articles demonstrate numerous innovative features to the benefit of readers, authors and all other users

Published since 1988 by the Austrian Herpetological Society (ÖGH, Österreichische Gesellschaft für Herpetologie), the renowned peer-reviewed, open-access Herpetozoa is added to the growing portfolio of international scientific journals published on the ARPHA scholarly platform, as a result of a new partnership with scholarly publisher and technology provider Pensoft.

Follow Herpetozoa on Twitter and Facebook.

As before, Herpetozoa welcomes original research articles, short contributions and reviews covering all aspects of the study of amphibians and reptiles. The papers are published in English, whereas a translation of the abstract into German may also be included. The journal operates a single-blind peer review policy.

Thanks to the fast-track and convenient publishing provided by ARPHA, each manuscript is carried through all stages from submission and reviewing to dissemination and archiving without ever leaving the platform’s collaboration-friendly online environment.

Right underneath the new sleek look and feel welcoming users from the journal’s homepage, there are a lot of high-tech perks to benefit authors, readers, reviewers and editors alike.

Furthermore, all publications are available in three formats (PDF, XML, HTML), complete with a whole set of semantic enhancements, so that the articles are easy to find, access and harvest by both humans and machines.


Editor-in-Chief of Herpetozoa, Dr Günter Gollmann states:

“We decided to move to Open Access online publishing to increase the visibility of our journal, and to speed up the publication process. The highly attractive presentation provided by Pensoft should boost attention for the papers we publish. While Herpetozoa welcomes contributions of any length on all topics in herpetology, I hope that authors will appreciate the suitability of the new format for data-rich studies in natural history. Such research is often dismissed as “too descriptive” by other international journals, but is essential for conservation of biodiversity.”

ARPHA’s and Pensoft’s founder and CEO Prof Lyubomir Penev says:

“I am pleased to see Herpetozoa having found its new home on the ARPHA platform amongst all Pensoft journals and other highly reputed academic titles from around the globe. With our own strong background in zoological sciences, I am certain that our partnership with Herpetozoa will be quick to prove fruitful to both of us, but most importantly, to all readers, authors, editors and reviewers alike.”

With its move to the open-access, technologically advanced scholarly publishing platform, Herpetozoa lines up next to historical and well-known society journals, including Deutsche Entomologische Zeitschrift, Alpine Entomology (previously Journal of the Swiss Entomological Society), Journal of Hymenoptera Research, Zoologia and others, which have all chosen to modernise with the help of ARPHA.

What’s new on Herpetozoa?

Amongst the first batch of articles published in Herpetozoa in partnership with ARPHA/Pensoft, there is an Italian study tracking the long-disputed origin of the Mediterranean-native common chameleon (Chamaeleo chamaeleo) back to its ancestors in North Africa and the Middle East. Another paper by a research team from Romania compares the effects of carnivore, vegetarian and omnivorous diets on the growth, development and mortality in tadpoles of the common toad. In their study of the South American frog species Leptodactylus fuscus, scientists from Universidade Federal de Mato Grosso do Sul (Brazil) compare the diet of a population living in the wild with another one, which inhabits an urban environment. Their aim was to determine the impact urbanisation could be having on this otherwise abundant amphibian.

Distribution of the common chameleon in Salento (southern Italy) in 2018. Black dots represent observation localities (Basso et al. 2019).
Study openly accessible at:
https://doi.org/10.3897/herpetozoa.32.e35611

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Herpetozoa is indexed in Biological Abstracts; BIOSIS (Previews); Current Contents – Agricultural, Science Citation Index (Expanded); Web of Science; Zoological Record (Plus). Currently, its Journal Impact Factor stands at 1.125.

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About the Austrian Herpetological Society:

The Austrian Herpetological Society (Österreichische Gesellschaft für Herpetologie, ÖGH) was founded in 1984 to advance all branches of herpetology. The society supports scientific research and promotes conservation of amphibians and reptiles, as well as their habitats. To raise public awareness of these animal groups, ÖGH organizes meetings and excursions and publishes the journals Herpetozoa and ÖGH-Aktuell.

WoRMS’ Top 10 Marine Species (2018): ZooKeys journal scores 5/10 in the prestigious yearly list

The World Register of Marine Species (WoRMS) announced the

Top 10 Marine Species of 2018 just in time for

Taxonomist Appreciation Day

What could be better timing to take a look back on the most spectacular animals described as new to science throughout 2018 than 19th March, Taxonomist Appreciation Day?

For the sixth time around, biologists from across the world are all hyped-up about this special date when we celebrate the experts who put things in order by giving names, identities and belonging to what the world has thought non-existent only a moment ago. After all, no sooner is a species formally acknowledged than it can be studied, understood and protected.

Having said that, at Pensoft and ZooKeys we’re immensely proud of becoming a prime publication choice for marine taxonomists from around the globe. Amongst them are the authors of not one or two, but FIVE exceptional animal curiosities, now recognised by a selected committee and the World Register of Marine Species (WoRMS), and featured in the TOP 10 Marine Species of 2018.

 

The “Japan Pig” which is also a… seahorse (Hippocampus japapigu)

Photo by Richard Smith.

We fail to find the obvious reason why locals diving in the waters of Hachijo-jima Island (Japan) had already likened this dazzling seahorse to a “tiny baby pig”, when a research team collected specimens and identified them as a species new to science. Naturally, the scientists assigned it with the name japapigu, which translates to “Japan Pig” in Japanese.

One thing is for sure, though, the stunning seahorse wouldn’t demand a degree in Zoology to attract anyone’s attention, had it not been for its expertise in camouflaging itself against the colourful algae-covered rocks.

News story by Douglas Main via National Geographic.

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Check out the study by Graham Short, California Academy of Sciences (USA), Dr Richard Smith, Pipefish Stickleback Specialist Group (UK), Dr Hiroyuki Motomura and Healy Hamilton, both of the Kagoshima University Museum (Japan), and David Harasti, Port Stephens Fisheries Institute, published in the open-access journal ZooKeys at: https://doi.org/10.3897/zookeys.779.24799.

 

The crab that chooses an animal ‘blanket’ over a shell (Paguropsis confusa)

Photo by DST/NRF ACEP – Spatial Solutions project team.

Sure, who would go for a rigid shell left behind by a random gastropod – just like “ordinary” hermit crabs do – when they could reach for a light, soft and elastic “blanket” instead?

That’s exactly what the blanket-hermit crab Paguropsis confusa and its sibling species have been doing as they evolved to live in a cosy symbiosis with sea anemones. While the translucent anemone peacefully “shares” the crab’s meals and grows its zoophytes around the soft-bodied crustacean, the latter is free to easily draw them up and down – as if they were a real silky duvet – and even completely cover its head whenever it feels threatened.

The crab species name is “con­fuso” in reference to its morphological resemblance to the closely related species Paguropsis typica. In fact, had it not been for the similarity, what we now call Paguropsis confuso would’ve most likely been described well over a century ago.

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Find more in the research article by Dr Rafael Lemaitre (Smithsonian’s National Museum of Natural History, USA), Dr Dwi Rahayu (Indonesian Institute of Sciences) and Dr Tomoyuki Komai (Natural History Museum and Institute, Japan) published in ZooKeys at: https://doi.org/10.3897/zookeys.752.23712

 

The ‘flower’ of Okinawa (Hana hanagasa)

Photo by Yee Wah Lau

Amidst ongoing talks and grim forecasts of declining coral reefs spelling demise for the world as we know it, the discovery of this endemic to Okinawa Island (Japan) flower-like octocoral comes as a stunning reminder of Nature’s supremacy.

Described as a new genus, as well as a species new to science, the octocoral was aptly named Hana hanagasa, where “Hana” translates to “flower” in Japanese, while “hanagasa” is a traditional Okinawan headpiece, crafted in the form of hibiscus and worn by female dancers at ceremonies.

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Find the study by the team of Yee Wah Lau and Dr James Reimer of the University of the University of the Ryukyus (Japan) and their colleagues Frank Robert Stokvis and Dr Leen van Ofwegen at Naturalis Biodiversity Center (the Netherlands) in ZooKeys at: https://doi.org/10.3897/zookeys.790.28875.

 

The distinctly hairy-foot shrimp (Odontonia bagginsi)

Illustration by Franz Anthony.

Upon writing up the description of this species of Indonesian shrimp, Leiden University’s then BSc student Werner de Gier is unlikely to have thought twice before coming up with the name bagginsi, as in Frodo and Bilbo Baggins – the most famous hobbits from J. R. R.Tolkien’s The Lord of the Rings and The Hobbit.                             

News story by Mike Wehner via New York Post.

After all, what the researcher was looking at was a creature tiny enough to call another marine invertebrate – a tunicate – its snug home. Also, it had extremely hairy feet, a feature that would require for the identification key for all members of the species group to be updated.

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Find the study by Werner de Gier and Dr Charles Fransen of the Naturalis Biodiversity Center published in ZooKeys at: https://doi.org/10.3897/zookeys.765.25277.

 

The ‘secretive’ dogfish shark from Hawai’i (Squalus hawaiiensis)

 

Photo by Dr Toby S. Daly-Engel.

 

One might think that an animal as large as a shark – especially if it’s the only shark species found in the waters of the Hawaiian Archipelago – would’ve “told” all its “secrets” by now, but that wasn’t the case with what we now refer to as the Hawaiian Spurdog.

Long mistaken for a stray population of a dogfish shark species originally from Japan, it wasn’t before US scientists deployed a range of elaborate tools used in species identification that it became apparent there was a previously unknown to science, short-ranged endemic shark trying to find shelter in Hawai’i.

Sadly, while the species is being depleted as bycatch, it has also demonstrated the lowest rate of genetic diversity known in a shark population to date.

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Find the study by Dr Toby Daly-Engel, Florida Institute of Technology, Amber Koch, University of West Florida, Dr James Anderson, University of Hawaii at Mānoa, and Charles Cotton and Dean Grubbs, both affiliated with the Florida State University Coastal and Marine Laboratory published in ZooKeys at: https://doi.org/10.3897/zookeys.798.28375.

 

Happy Taxonomist Appreciation Day from Pensoft!

Let us conclude with the words of ecologists and entomologist Dr Terry McGlynn, who started the Taxonomist Appreciation Day tradition in 2013:

“Even if you’re working on a single-species system, or are a theoretician, the discoveries and methods of systematists are the basis of your work,” he once told the Consortium of European Taxonomic Facilities (CETAF). “We need active work on taxonomy and systematics if our work is going to progress, and if we are to apply our findings. Without taxonomists, entire fields wouldn’t exist. We’d be working in darkness”.

FAIR biodiversity data in Pensoft journals thanks to a routine data auditing workflow

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

To avoid publication of openly accessible, yet unusable datasets, fated to result in irreproducible and inoperable biological diversity research at some point down the road, Pensoft takes care for auditing data described in data paper manuscripts upon their submission to applicable journals in the publisher’s portfolio, including Biodiversity Data Journal, ZooKeys, PhytoKeys, MycoKeys and many others.

Once the dataset is clean and the paper is published, biodiversity data, such as taxa, occurrence records, observations, specimens and related information, become FAIR (findable, accessible, interoperable and reusable), so that they can be merged, reformatted and incorporated into novel and visionary projects, regardless of whether they are accessed by a human researcher or a data-mining computation.

As part of the pre-review technical evaluation of a data paper submitted to a Pensoft journal, the associated datasets are subjected to data audit meant to identify any issues that could make the data inoperable. This check is conducted regardless of whether the dataset are provided as supplementary material within the data paper manuscript or linked from the Global Biodiversity Information Facility (GBIF) or another external repository. The features that undergo the audit can be found in a data quality checklist made available from the website of each journal alongside key recommendations for submitting authors.

Once the check is complete, the submitting author receives an audit report providing improvement recommendations, similarly to the commentaries he/she would receive following the peer review stage of the data paper. In case there are major issues with the dataset, the data paper can be rejected prior to assignment to a subject editor, but resubmitted after the necessary corrections are applied. At this step, authors who have already published their data via an external repository are also reminded to correct those accordingly.

“It all started back in 2010, when we joined forces with GBIF on a quite advanced idea in the domain of biodiversity: a data paper workflow as a means to recognise both the scientific value of rich metadata and the efforts of the the data collectors and curators. Together we figured that those data could be published most efficiently as citable academic papers,” says Pensoft’s founder and Managing director Prof. Lyubomir Penev.
“From there, with the kind help and support of Dr Robert Mesibov, the concept evolved into a data audit workflow, meant to ‘proofread’ the data in those data papers the way a copy editor would go through the text,” he adds.
“The data auditing we do is not a check on whether a scientific name is properly spelled, or a bibliographic reference is correct, or a locality has the correct latitude and longitude”, explains Dr Mesibov. “Instead, we aim to ensure that there are no broken or duplicated records, disagreements between fields, misuses of the Darwin Core recommendations, or any of the many technical issues, such as character encoding errors, that can be an obstacle to data processing.”

At Pensoft, the publication of openly accessible, easy to access, find, re-use and archive data is seen as a crucial responsibility of researchers aiming to deliver high-quality and viable scientific output intended to stand the test of time and serve the public good.

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

To explain how and why biodiversity data should be published in full compliance with the best (open) science practices, the team behind Pensoft and long-year collaborators published a guidelines paper, titled “Strategies and guidelines for scholarly publishing of biodiversity data” in the open science journal Research Ideas and Outcomes (RIO Journal).