Tag: scholarly journals

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Streamlined import of omics metadata from the European Nucleotide Archive (ENA) into an OMICS Data Paper manuscript

By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev

Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.

Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data  (https://doi.org/10.3897/rio.3.e12431). 

Fig. 1 Number of data papers published in Pensoft’s journals since 2011.

The data paper concept was initially based on the standard metadata descriptions, using the  Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blogpost.

Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.

How can authors publish omics data papers?

There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.

The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.

An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata. 

Fig. 2 Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA

Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:

  1. The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
  2. The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website,  click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
  3. The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
  4. The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript,  invite co-authors and then submit it for technical evaluation, peer review and publication. 

For a detailed description of authoring an OMICS data paper, please refer to the Author Guidelines: https://bdj.pensoft.net/about#OmicsDataPapers

Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields. 

We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.

To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.

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Pensoft to publish the paleontology and geobiology journal Zitteliana on behalf of SNSB

Following the recent contract between the State Natural History Collection of Bavaria (Staatliche Naturwissenschaftliche Sammlungen Bayerns or SNSB) and the scholarly publisher and technology provider Pensoft, the scholarly peer-reviewed, open-access journal on paleontology and geobiology Zitteliana will be published on the technologically advanced scholarly publishing platform ARPHA.

Expected later in 2020, Zitteliana will not only benefit from its own sleek-looking and user-friendly website, but will also enjoy a long list of services and high-tech features and human-provided services delivered from ARPHA’s signature fast-track, end-to-end publishing system. 

One thing that will greatly appeal to submitting authors, editors and reviewers is that the collaboration-focused ARPHA Platform supports manuscripts all the way from submission, peer review, editing, publication, dissemination and archiving within its online environment. On the other hand, to the benefit of readers, after publication, the articles are made available in PDF, machine-readable JATS XML formats, and semantically enriched HTML, which prompts discoverability, accessibility, citability and reusability. In addition, the journals will use all unique services offered by ARPHA, such as data publishing, linked data tables, semantic markup and enhancements, automated export of sub-article elements and data to aggregators, web-service integrations with more than 40 world-class indexing and archiving databases, sub-article-level usage metrics, and more.

Zitteliana is a scholarly journal covering all fields of paleontology and geobiology by the Bavarian State Collection of Palaeontology and Geology (SNSB): a research institution for natural history in Bavaria, comprising five State Collections. Initially limited to publications studying either the materials deposited in SNSB’s own collections, or topics related to the geology and palaeontology of Bavaria and adjacent regions, these days, Zitteliana welcomes articles in all fields of paleontology and geobiology. Encouraged are submissions on paleobiology, numerical paleontology, paleobiogeography, paleogenomics, palaeooceanography, biosedimentology, multiproxy and sequential stratigraphy, biodiversity research, and actuopaleontology, as well as contributions to the journal’s traditionally well-represented topics, such as paleontological taxonomy, systematics, phylogeny, and regional geology.

“It’s a great delight for Pensoft to be partnering such a prominent natural history institution like the SNSB and publish this particular journal of theirs. With our joint expertise and devotion, I am certain that we will successfully address major needs of the research community: readers, authors and their affiliates alike.”

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

The SNSB is the latest major German research institution to collaborate with Pensoft and choose ARPHA Platform for its journals. Since 2014, the Natural History Museum Berlin has trusted the publisher with its historical titles: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution. In 2017, Evolutionary Systematics, another prominent journal with a legacy in the field of zoology by the University of Hamburg followed suit. In 2020, we will be also seeing the move of three journals by the Senckenberg Nature Research Society: Arthropod Systematics & Phylogeny, Vertebrate Zoology and Geologica Saxonica.


About SNSB:

The Bavarian Natural History Collections (Staatliche Naturwissenschaftliche Sammlungen Bayerns, SNSB) are a research institution for natural history in Bavaria. They encompass five State Collections (zoology, botany, paleontology and geology, mineralogy, anthropology and paleoanatomy), the Botanical Garden Munich-Nymphenburg and eight museums with public exhibitions in Munich, Bamberg, Bayreuth, Eichstätt and Nördlingen.

Research conducted by over 30 permanent and 30 third-party funded scientists, currently employed at the SNSB, focuses mainly on the past and present bio- and geodiversity and the evolution of animals and plants. To achieve this, the institution keeps large scientific collections (more than 30,000,000 specimens). The collections and museums also play an instrumental role in public and academic education.

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

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 Journal published 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 Vegetazionevia 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.

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ARPHA Platform’s content integrated into ScienceOpen to take advantage of novel streams of science communication

The research discovery platform ScienceOpen and Pensoft Publishers have entered into a strategic collaboration 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 on ScienceOpen.

“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.

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Bulgaria’s publishers and scholars gathered to discuss the move of the national scientific journals to the global scene

The event was co-organised by Pensoft and the Bulgarian National Science Fund (BNSF) at the Ministry of Education and Science

Over one hundred representatives of Bulgarian scholarly journals and academic institutions attended a seminar, organised by the scientific publisher and technology provider Pensoft and the Bulgarian National Science Fund (BNSF) at the Ministry of Education and Science of Bulgaria. The meeting, themed “The Bulgarian scholarly journals in the global scientific environment – advancements in the publishing model, technological modernisation, indexing, dissemination and promotion,” took place in Sofia in September. 

In his speech, Prof. George Vaysilov, Director of the BNSF, highlighted the crucial role of scholarly publishing reformation in Bulgaria. He also answered various questions concerning the funding available to scientific journals.

“These events are useful for the Bulgarian scientific journals and the Bulgarian National Science Fund” will continue to participate in their organisation,” he said.

Prof. George Vaysilov gave a welcome speech before answering various questions from the attendees.
Photo by Pensoft.

In their talks, the Pensoft team addressed key topics and innovations related to journal publishing, management, dissemination and marketing in the digital era. They also showcased how these challenges are approached at the journals published via the scholarly Pensoft-developed ARPHA Platform. 

Main topics in the discussions were „Plan S”, the ongoing initiative for a global transition to immediate Open Access (Gold Open Access); exclusive digitisation; interoperability, findability and accessibility to online research items and data; traditional and alternative metrics for tracking journal impact; as well as the specifics about journal indexing. 


“Technological modernisation of the publishing process in an Open Access and Open Science environment” was the theme of Prof. Lyubomir Penev’s presentation. 
Photo by Pensoft.

Prof. Lyubomir Penev, Director and founder of Pensoft and ARPHA, added:

“In our own lifetimes, we’ve been the witnesses of a tremendous technological breakthrough on a global level. Not only does academia need not be left behind – its place is at the very forefront of such a revolution. This is exactly what we intend to do with ARPHA: to provide an all-rounded platform coupled with all the associated services, in order to provide the technological backbone needed by historical, as well as recently launched journals to make a stand on the international scene. Having listened to the questions and concerns of the Bulgarian publishers, I am able to confirm that the situation is not that different to what we see everywhere: there is the evident understanding of the situation and desire for a change. What is necessary is only a bit of practical know-how.”

The revolution in scholarly publishing in recent years. A part of Prof. Lyubomir Penev’s presentation.
Photo by Pensoft.

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As transparent as it gets! Four pricing plans & operating models from ARPHA available to OA academic journals

One size to fit them all? At ARPHA, we are well aware that it does not work like that in academia, let alone when it comes to accommodating individual scholarly journals from across the tremendously varied publishing landscape. 

This is why we have prepared four options to account for the specific aims and needs of ARPHA’s potential clients, while bearing in mind their resources and sustainability. 

In the spirit of transparency and openness, along with a comprehensive list of services that clarifies how each plan compares with the rest, we have provided the associated pricing ranges, where the total expenditure is easy to calculate, as it is based solely on the volume of published content. To support emerging publishers and prolific institutions, and express gratitude for their trust, we offer discounts for multiple journals joining ARPHA’s community.

Visit our website to see a detailed list of the services provided in our LITE, BASIC, ADVANCED and PREMIUM plans.

While Open Science initiatives, including OA2020 and Plan S, have clearly become the major talking points, academic institutions, societies and small-to-medium publishers from around the world are increasingly looking to chip in the growing community and make their own stand for science becoming truly efficient, responsible and inclusive by ensuring openness, transparency and FAIRness. But how do they do that when capped budgets, scarce human resources and lack of know-how in specific areas come into play? 

While one may be struggling with bringing together the right in-house expertise, another might be unable to keep track of the ‘top wanted’ integrations and services required for any state-of-the-art publication venue, and yet another might be encountering difficulties in communicating their otherwise ground-breaking published research to the public. In our experience, all of them are most likely experiencing difficulties with either the development of an advanced and user-friendly technological backbone or covering the associated costs.


ARPHA provides a highly automated, end-to-end publishing platform to ALL clients by default, which ensures that the research in their journals is just as easy to prepare and publish as it is to discover, access and reuse later on.

Here are the good news! ALL journals published on ARPHA Platform take advantage of our signature high-tech and easy-to-operate full-featured platform by default. What we mean, is that any journal benefits from an end-to-end, entirely online publishing solution, which takes care of the manuscripts all the way from submission and peer review to editing, publication, dissemination, indexing and archiving (see “The 5 Most Distinct Features of ARPHA”), while the annual maintenance could easily cost as little as a few thousands euros.

ARPHA stands for much more than a publishing platform.
It also comprises an extensive collection of services brought together in order to attend next-to-all demands associated with scholarly publishing.

On top of ARPHA’s user- and collaboration-friendly platform that allows for authors, reviewers and editors to easily and conveniently manage and track the progress of manuscripts, thereby ensuring that no technological pitfalls stand in the way to rapid and efficient distribution of scientific knowledge, our platform is continuously expanding its suite of services and features. This is also where one can find the major differences between the four plans offered by ARPHA.


With so many services and functionalities at hand, it was not that difficult for us to come up with four thought-through alternatives, and still ensure that ALL clients of ARPHA have their journals’ content published in a Findable, Accessible, Interoperable and Reusable manner. ga

As you can notice, even the lowest-priced LITE Plan features a plenty of useful and advanced perks, including a one-stop API end-point for distribution to 30+ international databases, metadata export to 12+ machine-readable formats, article sharing and usage statistics tools.

Assignment of DOIs to individual images is one of the perks exclusive in ARPHA’s PREMIUM plan (see pictured, available in Alpine Entomology). 


At the other end of the spectrum, ARPHA’s PREMIUM Plan adds top-notch features, such as assignment of Digital Object Identifiers (DOIs) to individual images, which in turn allows for the delivery of real-time usage metrics for each one of those.

Extensive marketing and promotional support, including an unlimited dissemination of press releases via the major global science news release platform Eurekalert! (AAAS), is also available to PREMIUM clients. Thus, a journal’s authors will not have to worry about their groundbreaking discoveries failing to reach the global public (e.g. news story “Scientists discover new Chinese firefly species” on SKY News, covering one of the latest publications in ZooKeys journal, and the associated press release on Eurekalert!).

News story via SKY News.

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Curious about how ARPHA could accommodate your journal(s)? 

Scroll down our pricing plans and operating models, and fill out the Get a Quote form. Shortly, we will be back in touch to discuss the best options for ARPHA to fit the specificity of your publishing project.

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Pensoft welcomes Neotropical Biology & Conservation to its open-access journal portfolio

Eleven studies in the first issue demonstrate the modernized look & feel of the Brazil-born journal, as provided by the scholarly publishing platform ARPHA

Launched by the Brazilian university Unisinos (Universidade do Vale do Rio dos Sinos) in 2006, the open-access, peer-reviewed Neotropical Biology & Conservation moves to the journal family of scholarly publisher and technology provider Pensoft.

Neotropical Biology & Conservation welcomes research and review articles, short communications and commentaries on the biology and behaviour of organisms from the tropical ecoregions of the Americas and the entire South America. Special emphasis is given to papers that demonstrate the application of conservation principles for natural resource management and policy. Manuscripts can be published in Portuguese, as well as English, where an English-language abstract is mandatory.

The journal is published three times a year, with the first 2019 issue already available on the new website. New research papers, part of the second issue, will be out next Monday (15th July).

New website for Neotropical Biology & Conservation

Beyond Neotropical Biology & Conservation‘s new glossy and user-friendly appearance, the Pensoft-developed scholarly platform ARPHA provides its signature fast-track, end-to-end publishing system to the benefit of its users: authors, reviewers and editors alike. Thereby, each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving ARPHA’s collaboration-centred online environment. The articles are available in PDF and machine-readable XML formats, so that they are easy to discover, access, cite and reuse.

Editor-in-Chief of Neotropical Biology & Conservation Dr Ana Maria Leal-Zanchet, says:

“It’s an honour for the Editorial board of Neotropical Biology & Conservation that the journal becomes a member of the Pensoft/ARPHA team. This journal was born as Acta Biologica Leopoldensia, which was published by Unisinos between 1979 and 2005. Since 2006 Neotropical Biology & Conservation continued the tradition of this former journal, publishing articles from all around Brazil, and even enhancing its coverage to other parts of the Neotropics. In recent years, the scientific community that uses our journal as a venue to disseminate their research results has been continuously increasing. We maintain our commitment to disseminate scientific findings through open access and to continue pursuing a sustainable international growth. I am sure that the user-friendly ARPHA’s publishing system and the great support of the Pensoft team will please authors, reviewers and the Editorial board of the journal, enhancing the efficiency, quality and swiftness of publishing, as well as the international visibility of Neotropical Biology & Conservation.”

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

“I’m delighted to welcome Neotropical Biology & Conservation to the Pensoft/ARPHA family, where the journal not only feels at home amongst predominantly biodiversity-themed titles, but also comes to complement another two Brazil-born journals: Check List, which publishes biogeographical data, especially for the use of biodiversity conservation, and Zoologia: mostly focusing on systematics, evolution and taxonomy in the field of Zoology. With this kind of background and the constantly expanding high-tech functions of ARPHA, I’m certain that we are fully equipped to build on the image and success of Neotropical Biology & Conservation.”

What’s on in the first issue?

Amongst the 11 articles in the first issue of Neotropical Biology & Conservation, there is the study by Dr Lucas Porto (Federal University of Rio Grande do Sul) and Dr Ana Maria Rui (Universidade Federal de Pelotas), which observes Crab-eating and Pampas foxes in southern Brazil for a year to compare the diets and habitat uses of the two sympatric species. Curiously, the canids demonstrated a high overlap of their diets at all times, with the exception of autumn.

Another paper, authored by a research team from the Federal Institute of Education, Science and Technology of Goiano and the Federal University of Goiás, describes the frequency, occurrence status and activity period of the most common medium- and large-sized mammals living in the world’s most biodiverse savanna: Brazil’s Cerrado. Namely, subjects of the study were the Giant anteater, Nine-banded armadillo, South American tapir, Crab-eating fox and Lowland paca, where the largest species were found to have the greatest variation in time period of activity.

A collaborative work at the Federal University of Pernambuco, University of Brasília and the Rural Federal University of Pernambuco, reports important observations of the unexpectedly diverse bat fauna in an urban environment located in the Atlantic Forest, northeastern Brazil. Between May 2006 and April 2007, the researchers captured 950 bats identified to 16 species and five families.

The first 2019 issue of Neotropical Biology and Conservation.

Follow Neotropical Biology & Conservation on Twitter and Facebook.

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All ARPHA-hosted 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.

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Moscow State University’s journal Population and Economics now published on ARPHA platform

The first 2019 issue of the journal Population and Economics is now published and demonstrates a brand new look-and-feel and high-tech perks

Population and Economics is the latest renowned journal to feature on the growing portfolio of open-access titles making use of the innovative scholarly platform ARPHA. Having taken advantage of ARPHA’s white-label publishing solution, the journal accommodates a long list of high-tech novelties which benefit authors, readers and editors alike. Marking the new partnership is the first 2019 issue of the journal, now available on its brand new website.

Population and Economics is the latest renowned journal to feature on the growing portfolio of open-access titles making use of the innovative scholarly publishing platform ARPHA, developed by 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.

Published by the Faculty of Economics at Lomonosov Moscow State University with the support of Derzhava Bank, Population and Economics has the mission to provide the international community with a scholarly platform facilitating the exchange of theoretical and practical knowledge in the study of population development, as well as results from interdisciplinary economic and demographic research.

From now on, further manifesting its dedication to sharing scientific findings on a global scale, Population and Economics is to publish articles in three formats (PDF, XML, HTML) enriched with a whole set of semantic enhancements, so that the papers, along with their data, are easy to discover, access and harvest by both humans and machines from around the world.

The journal is published in English, however, for the convenience of its large audience in Russia, articles are also available in Russian in PDF format. These are accessible from the corresponding paper’s webpage and registered under the same Digital Object Identifier (DOI).

Amongst the other high-tech perks delivered by ARPHA are sophisticated article- and sub-article-level metrics, such as those provided by discovery and analytics-specialised partner Dimensions. The latter allows for the reader to easily look up the publications that have cited the particular paper, as well as their distribution over time and across research categories.

Additionally, beneath the sleek and modern interface, there is a long list of services at the disposal of all users of Population and Economics: editors, reviewers, authors and readers alike. In order to ensure that articles are submitted, reviewed, published and disseminated rapidly and conveniently, manuscripts undergo the entire review and publication processes within ARPHA’s seamless online environment.

Submissions of research and review articles, research notes and short communications addressing a range of interdisciplinary topics are all invited at Population and Economics. The journal welcomes analyses and forecasts in the fields of demography, development and reproduction of population, economic demography, health economics, household economics, the economics of inequality, spatial demography and economy, demographic and socio-economic behaviour, applied demography, population policy and social policies amongst others.

The journal operates single-blind peer review, where the reviewers are encouraged to disclose their identities.

All publications are indexed by the Russian Scientific Citation Index (RSCI) and Google Scholar, as well as BASE, CNKI, CrossRef, Dimensions, Mendeley, Microsoft Academic, Naviga (Softweco), OCLC WorldCat, OpenAIRE, OpenCitations, ReadCube, Unpaywall. The articles will be archived at CLOCKSS, Zenodo and Portico.

“I am delighted to see our collaboration with Population and Economics already in the flesh,” says ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev. “Now that the first ARPHA-published issue of this valued journal is live, I can say with confidence that we are observing the wonderful beginning of a prolific and future-oriented partnership.”

Editor-in-Chief Prof. Irina Kalabikhina adds: “Through our collaboration with the wonderful high-technology publishing platform ARPHA, we are opening a new page in the life of Population and Economics. Published since 2017 in English and Russian, our journal has been bringing authors and readers together, in order to support an interdisciplinary approach to the study of population economics. I am certain that our further cooperation will make the journal more recognisable within the global scholarly community, expand the geography of the participants in the scientific discussions and secure access to novel research results.”

About Faculty of Economics, Lomonosov Moscow State University

Founded in 1941, the Faculty of Economics continues the centuries-old tradition of economic education in Russia, being one of the leading university-level centres in the field of Economics. The faculty combines fundamental education and professional training in order to develop its students’ analytical skills and creative thinking, thereby helping its graduates to adapt quickly and successfully to the requirements of any job in the field of economics.

About Lomonosov Moscow State University

Founded in 1755 by Russian polymath, scientist and writer Mikhail Lomonosov, the university is currently the highest-ranking Russian educational institution, according to the 2018 QS World University Rankings. It is also considered to be the most prestigious university in the former Soviet Union. Every year Moscow University enrolls about 4 000 international students and postgraduates from all over the world.

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MEPhI’s Nuclear Energy and Technology journal moves to the OA scholarly platform ARPHA

The first issue since the transition is now live on NUCET’s new website

Devoted to an extensive range of research fields within the domain of nuclear science, the open access, peer-reviewed Nuclear Energy and Technology (NUCET) journal moves to the journal publishing platform ARPHA, developed by Pensoft, in order to provide a whole set of novel technological advancements to its users: readers, authors and editors alike.

The first journal issue since the transition is now live on NUCET‘s new website and features a total of 12 research articles, covering topics including nuclear power plant operation, reactor physics and thermal hydraulics.

Launched in September 2015 by the internationally recognised National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), the journal has since been providing an open-access, peer-reviewed English-language outlet for original research, ideas and developments for scientists from around the globe. The journal is managed by the Institute of Nuclear Physics and Technology of the National Research Nuclear University MEPhI.

Areas covered by NUCET feature:

  • Reactor physics;
  • Heat transfer and fluid dynamics;
  • Nuclear safety and radiation protection;
  • Nuclear physics, fusion and radiation application;
  • Nuclear fuel cycle and radioactive waste management;
  • Nuclear fuel and reactor materials;
  • Nuclear policy, economics and education issues.

Homepage of the new website of the Nuclear Energy and Technology (NUCET) journal.

Beyond the sleek new website, ARPHA platform provides various high-tech perks to ensure that the entire publishing process – beginning with manuscript submission and continuing all the way to the dissemination, archiving and indexing of the article’s content and metadata – takes place within its single online environment.

With each article being simultaneously published in semantically-enriched PDF, HTML and XML formats, the publications are easy to discover, access and harvest by both researchers and computers. As a result, research published in NUCET is easier to cite, reuse, build on and replicate.

“I’m delighted to welcome NUCET to the growing portfolio of scholarly journals published on ARPHA,” says ARPHA’s and Pensoft’s founder and CEO Prof. Lyubomir Penev. “As the first nuclear science journal joining ARPHA, I believe that NUCET could easily be regarded as a harbinger of a promising new area of collaboration and enterprise.”

“Today we are celebrating an important event – the first issue of the journal Nuclear Energy and Technology on the ARPHA platform.” As the Rector of the National Research Nuclear University MEPhI and NUCET’s Editor-in-Chief Prof. Mikhail Strikhanov says: “NUCET is an English-language periodical of the MEPhI that is promoting the results of our research to the worldwide scientific community”.

He also explains that the choice of platform was not accidental:

Prof. Mikhail Strikhanov, Rector of the National Research Nuclear University MEPhI and Editor-in-Chief of NUCET

“We have analyzed many publishing platforms and explored their strengths and weaknesses. ARPHA publishes many high-quality journals, and it is very important for us to be the first in the field of nuclear physics there. We are looking forward to continuing cooperation with Pensoft, and we are confident that with the help of ARPHA NUCET has an incredible future and the quality of its materials will be at a high level”.

Nuclear Energy and Technology (NUCET) is the fifth Russian journal to move to ARPHA Platform, following Comparative Cytogenetics, Research results in Pharmacology, Russian Journal of Economics and Arctic Environmental Research.

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Follow Nuclear Energy and Technology (NUCET) journal on Twitter.

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About National Research Nuclear University MEPhI:

The National Research Nuclear University MEPhI is a leading Russian university and a research and educational centre with honourable traditions and clear vision of the future.

It empowers the world’s best nuclear technological experts and talented students to produce secure and stable energy, excel in creating applicable science, boost human capital and economic output in various fields, support industry and business and be innovative and creative.

MEPhI is proud of its ambitious and skilled experts in science and engineering who have graduated at the university since its establishment in 1942, including six Nobel laureates, who have themselves later contributed to the educational process and research activities at the institute.