Upcoming Special Issue of Biodiversity Data Journal to feature data papers on European Russia

Partners GBIF, FinBIF and Pensoft to support publication of data papers that describe datasets from Russia west of the Ural Mountains

Original post via GBIF

GBIF—the Global Biodiversity Information Facility—in collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, are happy to issue a call for authors to submit and publish data papers on European Russia (west of the Urals) in an upcoming special issue of Biodiversity Data Journal (BDJ).

Between now and 31 August 2020, the article processing fee (normally €450) will be waived for the first 20 papers, provided that the publications are accepted and meet the following criteria that the data paper describes a dataset:

The manuscript must be prepared in English and is submitted in accordance with BDJ’s instructions to authors by 31 August 2020. Late submissions will not be eligible for APC waivers.

Sponsorship is limited to the first 20 accepted submissions meeting these criteria on a first-come, first-served basis. The call for submissions can therefore close prior to the stated deadline of 31 August. Authors may contribute to more than one manuscript, but artificial division of the logically uniform data and data stories, or “salami publishing”, is not allowed.

BDJ will publish a special issue including the selected papers by the end of 2020. The journal is indexed by Web of Science (Impact Factor 1.029), Scopus (CiteScore: 1.24) and listed in РИНЦ / eLibrary.ru

For non-native speakers, please ensure that your English is checked either by native speakers or by professional English-language editors prior to submission. You may credit these individuals as a “Contributor” through the AWT interface. Contributors are not listed as co-authors but can help you improve your manuscripts.

In addition to the BDJ instruction to authors, it is required that datasets referenced from the data paper a) cite the dataset’s DOI and b) appear in the paper’s list of references.

Authors should explore the GBIF.org section on data papers and Strategies and guidelines for scholarly publishing of biodiversity data. Manuscripts and datasets will go through a standard peer-review process.

To see an example, view this dataset on GBIF.org and the corresponding data paper published by BDJ.

Questions may be directed either to Dmitry Schigel, GBIF scientific officer, or Yasen Mutafchiev, managing editor of Biodiversity Data Journal.

Definition of terms

Datasets with more than 5,000 records that are new to GBIF.org

Datasets should contain at a minimum 5,000 new records that are new to GBIF.org. While the focus is on additional records for the region, records already published in GBIF may meet the criteria of ‘new’ if they are substantially improved, particularly through the addition of georeferenced locations.

Justification for publishing datasets with fewer records (e.g. sampling-event datasets, sequence-based data, checklists with endemics etc.) will be considered on a case-by-case basis.

Datasets with high-quality data and metadata

Authors should start by publishing a dataset comprised of data and metadata that meets GBIF’s stated data quality requirement. This effort will involve work on an installation of the GBIF Integrated Publishing Toolkit.

Only when the dataset is prepared should authors then turn to working on the manuscript text. The extended metadata you enter in the IPT while describing your dataset can be converted into manuscript with a single-click of a button in the ARPHA Writing Tool (see also Creation and Publication of Data Papers from Ecological Metadata Language (EML) Metadata. Authors can then complete, edit and submit manuscripts to BDJ for review.

Datasets with geographic coverage in European Russia west of the Ural mountains

In correspondence with the funding priorities of this programme, at least 80% of the records in a dataset should have coordinates that fall within the priority area of European Russia west of the Ural mountains. However, authors of the paper may be affiliated with institutions anywhere in the world.

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Data audit at Pensoft’s biodiversity journals

Data papers submitted to Biodiversity Data Journal, as well as all relevant biodiversity-themed journals in Pensoft’s portfolio, undergo a mandatory data auditing workflow before being passed down to a subject editor.

Learn more about the workflow here:
https://www.eurekalert.org/pub_releases/2019-10/pp-aif101819.php.

Viticulture Data Journal: Non-conventional papers foster Open Science & sustainability

Non-conventional, yet pivotal research results: data, models, methods, software, data analytics pipelines and visualisation methods, related to the field of viticulture, find a place in a newly launched, open-access and peer-reviewed Viticulture Data Journal (VDJ). The journal went live with the publication of an introductory editorial and a data paper.

The publishing venue is one of the fruits borne during the collaboration between scholarly publisher and technology provider Pensoft, its self-developed ARPHA Platform and the EU project AGINFRA+, whose mission is to provide a sustainable channel and data infrastructure for the use of cooperating, but not fully connected user communities working within the agricultural and food sciences. 

The novel journal brings together a wide range of topics related to the field of viticulture: from genetic research, food safety of viticultural products to climate change adaptation of grapevine varieties through grape specific research. Amongst these are:

  • Phenotyping and genotyping
  • Vine growth and development
  • Vine ecophysiology
  • Berry yield and composition
  • Genetic resources and breeding
  • Vine adaptation to climate change, abiotic and biotic stress
  • Vine propagation
  • Rootstock and clonal evaluation
  • Effects of field practices (pruning, fertilization etc.) on vine growth and quality
  • Sustainable viticulture and environmental impact
  • Ampelography
  • Plant pathology, diseases and pests of grapevine
  • Microbiology and microbiological risk assessment
  • Food safety related to table grapes, raisins, wine, etc.

With the help of the ARPHA Platform’s signature writing tool, authors are able to use a set of pre-defined, yet flexible manuscript templates: Data Paper, Methods, Emerging Techniques, Applied Study, Software Description, R Package and Commentary. Furthermore, thanks to the advanced collaborative virtual environment provided by the tool, authors, but also reviewers, editors and other invited contributors enjoy the convenience of working within the same consolidated online file all the way from the authoring and peer review stages to copy editing and publication.

“The Viticulture Data Journal was created to respond to the major technological and sociological changes that have influenced the entire process of scholarly communication towards Open Science,”

explain the editors.

“The act of scientific publishing is actually the moment when the long effort of researchers comes to light and can be assessed and used by other researchers and the wider public. Therefore, it is little wonder that the main arena of transition from Open Access to Open Science was actually the field of academic publishing,”

they add.

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The first research publication made available in VDJ is a data paper by the research team from Agricultural University of Athens: Dr Katerina Biniari, Ioannis Daskalakis, Despoina Bouza and Dr Maritina Stavrakaki. In their study, they assess and compare both the qualitative and quantitative characters of the grape cultivars ‘Mavrodafni’ and ‘Renio’, grown in different regions of the Protected Designation of Origin Mavrodafni Patras (Greece). The associated dataset, containing the mechanical properties, the polyphenolic content and the antioxidant capacity of skin extracts and must of berries of the two cultivars, is available to download as supplementary material from the article.  

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During the AGINFRA+ project, ARPHA has been extended to be used from the AGINFRA+ Virtual Research Environment (VRE), which would allow the authors to use the VRE as an additional gate to the AWT and the journal, as well as to benefit from the integration of AWT with several other services offered by the AGINFRA+ platform. The AGINFRA+ platform has been designed as a Gateway providing online access through a one-stop endpoint to services, aiming at the integration of the traditional narrative of research articles with their underlying data, software code and workflows.

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Viticulture Data Journal is indexed by Altmetric, CrossRef, Dimensions, EBSCOhost, Google Scholar, Mendeley, Microsoft Academic, Naviga (Suweco), OCLC WorldCat, OpenAIRE, OpenCitations, ReadCube, Ulrichsweb™, Unpaywall; and archived at CLOCKSS and Zenodo

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Follow Viticulture Data Journal on Twitter and Facebook.

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.


As transparent as it gets! Five 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 five 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 what services our LITE, BASIC, STANDARD, ADVANCED and PREMIUM plans provide and how much each of them would cost for your individual case.  

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 five plans offered by ARPHA.

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

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.

New journal One Ecosystem: Innovation in ecology and sustainability research publishing

Focused on the fields of ecology and sustainability, One Ecosystem is an innovative open access scholarly journal that goes beyond the conventional research article publication. Launched in January 2016, the new journal is now open for submissions ranging across the entire research cycle, including data, models, methods, workflows, results, software, perspectives and policy recommendations.

Ecosystem services, Ecology and Sustainability are research areas that address highly relevant scientific and societal topics. One Ecosystem aims to respond to the newest developments in scholarly publishing, adapting them for and applying them to these fields.

The journal offers a wide set of article templates, including domain-specific ones, such as Ecosystem services mapping, Ecological models or Environmental monitoring, allowing scientists to publish and get credit for their work at any stage of the research cycle. Through the technologically advanced ARPHA publishing platform and innovative publishing model, all data that underpin a given study will be made free to everyone and integrated into relevant and domain-specific global data repositories.

“We need better incentives for scientists who want to share their data. One Ecosystemprovides such incentives by linking peer review to open data” adds Joachim Maes, European Commission – Joint Research Centre.

“We believe that open access to all the relevant products of the scientific cycle is key to both scientific advancement, and innovation in the real world. With One Ecosystem we aim at fostering open exchange of information to address sustainability challenges.” – Deputy Editor-in-Chief Dr. Davide Geneletti, University of Trento.

Open access to content and data is quickly becoming the prevailing model in academic publishing and research funding schemes. By making research outputs public, the new journal opens up new mechanisms for integration of information, collaboration, appraisal, and dissemination. Committed to openness and innovation, One Ecosystem offers a novel community-based peer-review introduced for the first time in these academic disciplines. The journal gives authors and reviewers the opportunity to opt for an entirely open review process.

Making use of the unique ARPHA Writing Tool, One Ecosystem does not only enable authors to prepare their manuscripts directly within the system, but also allows to submit pre-submission reviews from the very start. These reviews or supporting statements from experts in the subject will facilitate the manuscript evaluation and speed up the publishing process.

“With One Ecosystem we want to accelerate scientific progress in the frontier research fields of ecology and sustainability. We are convinced that this new format of writing, reviewing and open access publishing of scientific findings is the future”, explains the Editor-in Chief of One Ecosystem – Dr. Benjamin Burkhard, University of Kiel.

“At Pensoft we have been committed to innovating scientific publishing for years. In One Ecosystem, we have collected all our knowledge and experience to provide scientists in the fields of ecology and sustainability with a conceptually new journal that will give them the opportunity to publish outcomes and collaborate with the community in a new open and more efficient way”, comments Prof. Lyubomir Penev, Founder and Managing Director at Pensoft.

Follow One Ecosystem on Twitter | Facebook

Import of Specimen or Occurrence Records Into Taxonomic Manuscripts

Repositories and data indexing platforms, such as GBIFBOLD systems, or iDigBio hold documented specimen or occurrence records along with their record ID’s. In order to streamline the authoring process, save taxonomists’ time, and provide a workflow for peer-review and quality checks of raw occurrence data, the ARPHA team has introduced an innovative feature that makes it possible to easily import specimen occurrence records into a taxonomic manuscript (see Fig. 1).

For the remainder of this post we will refer to specimen data as occurrence records, since an occurrence can be both an observation in the wild, or a museum specimen.

Figure1

Fig. 1: Workflow for directly importing occurrence records into a taxonomic manuscript.

Until now, when users of the ARPHA writing tool wanted to include occurrence records as materials in a manuscript, they would have had to format the occurrences as an Excel sheet that is uploaded to the Biodiversity Data Journal, or enter the data manually. While the “upload from Excel” approach significantly simplifies the process of importing materials, it still requires a transposition step – the data which is stored in a database needs to be reformatted to the specific Excel format. With the introduction of the new import feature, occurrence data that is stored at GBIFBOLD systems, or iDigBio, can be directly inserted into the manuscript by simply entering a relevant record identifier.

The functionality shows up when one creates a new “Taxon treatment” in a taxonomic manuscript prepared in the ARPHA Writing Tool. The import functions as follows:

  1. the author locates an occurrence record or records in one of the supported data portals;
  2. the author notes the ID(s) of the records that ought to be imported into the manuscript (see Fig. 2, 3, and 4 for examples);
  3. the author enters the ID(s) of the occurrence records in a form that is to be seen in the materials section of the species treatment, selects a particular database from a list, and then simply clicks ‘Add’ to import the occurrence directly into the manuscript.

In the case of BOLD Systems, the author may also select a given Barcode Identification Number (BIN; for a treatment of BIN’s read below), which then pulls all occurrences in the corresponding BIN (see Fig. 5).

Figure 2       Figure 3

Fig. 2: (Left) An occurrence record in iDigBio. The UUID is highlighted; Fig. 3: (Right) An occurrence record in GBIF. The GBIF ID and the Occurrence ID is highlighted. (Click on images to enlarge)

Figure 4       Figure 5

Fig. 4: (Left) An occurrence record in BOLD Systems. The record ID is highlighted.; Fig. 5:  (Right) All occurrence records corresponding to a OTU. The BIN is highlighted. (Click on images to enlarge)

We will illustrate this workflow by creating a fictitious treatment of the red moss, Sphagnum capillifolium, in a test manuscript. Let’s assume we have started a taxonomic manuscript in ARPHA and know that the occurrence records belonging to S. capillifolium can be found in iDigBio. What we need to do is to locate the ID of the occurrence record in the iDigBio webpage. In the case of iDigBio, the ARPHA system supports import via a Universally Unique Identifier (UUID). We have already created a treatment for S. capillifolium and clicked on the pencil to edit materials (Fig. 6). When we scroll all the way down in the pop-up window, we see the form which is displayed in the middle of Fig. 1.

Figure 6

Fig. 6: Edit materials.

From here, the following actions are possible:

  • insert (an) occurrence record(s) from iDigBio by specifying their UUID’s (universally unique identifier) (Fig.2);
  • insert (an) occurrence record(s) from GBIF by entering their GBIF ID’s (Fig.3);
  • insert (an) occurrence record(s) from GBIF by entering their occurrence ID’s (note that unfortunately not all GBIF records have an occurrence ID, which is to be understood as some sort of universal identifier) (Fig. 3);
  • insert (an) occurrence record(s) from BOLD by entering their record ID’s (Fig. 4);
  • insert a set of occurrence records from BOLD belonging to a BIN (barcode index number) (Fig. 5).

In this example, select the fifth option (iDigBio) and type or paste the UUID b9ff7774-4a5d-47af-a2ea-bdf3ecc78885 and click Add. This will pull the occurrence record for S. capillifolium from iDigBio and insert it as a material in the current paper (Fig. 6). The same workflow applies also to the aforementioned GBIF and BOLD portals.

Figure 7

Fig. 7: Materials after they have been imported.

This workflow can be used for a number of purposes but one of its most exciting future applications is the rapid re-description of Linnaean species, or new morphological descriptions of species together with DNA barcode sequences (a barcode is a taxon-specific highly conserved gene that provides enough inter-species variation for statistical classification to take place) using the  Barcode Identification Numbers (BIN’s) underlying an Operational Taxonomic Units (OTU). If a taxonomist is convinced that a species hypothesis corresponding to OTU defined algorithmically at  BOLD systems clearly presents a new species, then he/she can import all specimen records associated with that OTU via inserting that OTU’s BIN ID in the respective fields.

Having imported the specimen occurrence records, the author needs to define one specimen as holotype of the news species, other as paratypes, and so on. The author can also edit the records in the ARPHA tool, delete some, or add new ones, etc.

Not having to retype or copy/paste species occurrence records, the authors save a lot of efforts. Moreover, they automatically import them in a structured Darwin Core format, which can easily be downloaded from the article text into structured data by anyone who needs the data for reuse.

Another important aspect of the workflow is that it will serve as a platform for peer-review, publication and curation of raw data, that is of unpublished individual data records coming from collections or observations stored at GBIF, BOLD and iDigBio. Taxonomists are used to publish only records of specimens they or their co-authors have personally studied. In a sense, the workflow will serve as a “cleaning filter” for portions of data that are passed through the publishing process. Thereafter, the published records can be used to curate raw data at collections, e.g. put correct identifications, assign newly described species names to specimens belonging to the respective BIN and so on.

Additional Information:

The work has been partially supported by the EC-FP7 EU BON project (ENV 308454, Building the European Biodiversity Observation Network) and the ITN Horizon 2020 project BIG4(Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.