Linking FAIR biodiversity data, NEW article collection in BDJ

Supported by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project, the collection at Biodiversity Data Journal will provide APC waivers for up to 100 publications

A new article collection, dedicated to linked FAIR biodiversity data was announced by the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project.

The BiCIKL project is dedicated to building new communities of key research infrastructures, researchers, citizen scientists and other stakeholders by using linked and FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing and identification of taxa, to final publication in advanced, human- and machine-readable, reusable scholarly articles.

Supported by BiCIKL, the upcoming collection at BDJ will provide an exciting opportunity for biodiversity researchers to enjoy free and technologically advanced publication for up to 100 scholarly articles.

The collection will welcome research articles, data papers, software descriptions, and methodological/theoretical papers that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

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The journal is still looking for guest editors to join the core team. If you are interested, please let us know at bdj@pensoft.net.

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In this collection, the authors will need to ensure that their narratives comply with the community-agreed standards for terms, ontologies and vocabularies. Additionally, they will be required to use explicit persistent identifiers, where such are available. 

Here are several examples of research questions concerning semantically enriched biodiversity data: 

  1. How linking taxa or OTUs to external data in my study will contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
  2. How mine and other researchers’ data and narratives (e.g. specimen records, sequences, traits, biotic interactions etc.) can be re-used to support more extensive and data-rich studies? 
  3. How to streamline taxon descriptions and inventories, including such based on genomic and barcoding data? 
  4. How general conclusions, assertions and citations in my article can be expressed in a formal, machine-actionable language? 
  5. Other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR data.

Conditions for publication and types of articles:

  • Manuscripts must use data from at least two of the BiCIKL’s partnering research infrastructures. Highly welcome are also submissions that include data from research infrastructures that are not part of BiCIKL.
  • Taxonomic papers (e.g. descriptions of new species) must contain persistent identifiers for the holotype, paratypes and the majority of the specimens used in the study.
  • New species descriptions using data associated with a particular Barcode Identification Number (BIN) imported directly from BOLD via the ARPHA Writing Tool are encouraged.
  • Individual specimen records imported directly from BOLD, GBIF or iDigBio into the manuscript are strongly encouraged.
  • Hyperlinked in-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome.
  • Other terms of value hyperlinked to external resources are encouraged.
  • Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s guidelines.
  • Theoretical or methodological papers on linking of FAIR biodiversity data are eligible for the BiCIKL collection if they provide examples and use cases.
  • Data papers or software descriptions are eligible if they use data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.


You can find full information about the eligibility criteria in the Open Call published on the BiCIKL’s website, or can contact us at bdj@pensloft.net.

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Natural History Museum of Berlin’s journal Fossil Record started publishing on ARPHA Platform

Fossil Record – the paleontological scholarly journal of the Natural History Museum of Berlin (Museum für Naturkunde Berlin) published its first articles after moving to the academic publisher Pensoft and its publishing platform ARPHA Platform in late 2021. The renowned scientific outlet – launched in 1998 – joined two other historical journals owned by the Museum: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution, which moved to Pensoft back in 2014.

Fossil Record – the paleontological scholarly journal of the Natural History Museum of Berlin (Museum für Naturkunde Berlin) published its first articles after moving to the academic publisher Pensoft and its publishing platform ARPHA in late 2021. The renowned scientific outlet – launched in 1998 – joined two other historical journals owned by the Museum: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution, which moved to Pensoft back in 2014.

Published in two issues a year, the open-access scientific outlet covers research from all areas of palaeontology, including the taxonomy and systematics of fossil organisms, biostratigraphy, palaeoecology, and evolution. It deals with all taxonomic groups, including invertebrates, microfossils, plants, and vertebrates.

As a result of the move to ARPHA, Fossil Record utilises the whole package of ARPHA Platform’s services, including its fast-track, end-to-end publishing module, designed to appeal to readers, authors, reviewers and editors alike. A major advantage is that the whole editorial process, starting from the submission of a manuscript and continuing into peer review, editing, publication, dissemination, archiving and hosting, happens within the online ecosystem of ARPHA. 

As soon as they are published, the articles in Fossil Record are available in three formats: PDF, machine-readable JATS XML and semantically enriched HTML for better and mobile-friendly reader experience. 

The publications are equipped with real-time metrics on both article and sub-article level that allow easy access to the number of visitors, views and downloads for every article and each of it’s figures, tables or supplementary materials. In their turn, the semantic enhancements do not only allow for easy navigation throughout the text and quick access to cited literature and the article’s own citations, but also tag each taxon that appears in the paper to provide links to further information concerning its occurrences, genomics, nomenclature, treatments and more as available from various databases.      

The first five papers – now available on the brand new journal website powered by ARPHA – already demonstrate the breadth of topics covered by Fossil Record, including systematics, paleobiogeography, palaeodiversity and morphology, as well as the international appeal of the scholarly outlet. The articles are co-authored by collaborative research teams representing ten countries and spanning three continents: Europe, Asia and Africa.

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About the Natural History Museum of Berlin:

The “Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science” is an integrated research museum within the Leibniz Association. It is one of the most important research institutions worldwide in the areas of biological and geological evolution and biodiversity.

The Museum’s mission is to discover and describe life and earth – with people, through dialogue. As an excellent research museum and innovative communication platform, it wants to engage with and influence the scientific and societal discourse about the future of our planet, worldwide. Its vision, strategy and structure make the museum an excellent research museum. The Natural History Museum of Berlin has research partners in Berlin, Germany and approximately 60 other countries. Over 700,000 visitors per year as well as steadily increasing participation in educational and other events show that the Museum has become an innovative communication centre that helps shape the scientific and social dialogue about the future of our earth. 

Fossil Record, a Natural History Museum of Berlin journal moves to ARPHA

Having been publishing its historically renowned Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution in partnership with Pensoft since 2014, the Museum extends the collaboration by moving a third signature journal

Having been publishing its historically renowned scientific journals Deutsche Entomologische Zeitschrift (DEZ) and Zoosystematics and Evolution (ZSE) in partnership with the scholarly publisher Pensoft and its ARPHA Platform since 2014, the Natural History Museum of Berlin (Museum für Naturkunde Berlin) now extends the collaboration by moving a third signature journal: Fossil Record

Launched in 1998 under the name Mitteilungen aus dem Museum für Naturkunde Berlin, Geowissenschaftliche Reihe, Fossil Record is the Natural History Museum of Berlin’s palaeontological journal. Published in two issues a year, the open-access scientific outlet covers research from all areas of palaeontology, including the taxonomy and systematics of fossil organisms, biostratigraphy, palaeoecology, and evolution. It deals with all taxonomic groups, including invertebrates, microfossils, plants, and vertebrates.

Following its move to ARPHA, Fossil Record is to utilise the whole package of ARPHA Platform’s services, including its fast-track, end-to-end publishing module, designed to appeal to readers, authors, reviewers and editors alike. 

With ARPHA, each submitted manuscript is carried through the review, editing, publication, dissemination and archiving stages without leaving the platform’s collaboration-centred online environment. The articles are made available in PDF and machine-readable JATS XML formats, as well as semantically enriched HTML for better and mobile-friendly reader experience. 

As a result, the journal’s articles are as easy to discover, access, reuse and cite as possible. Once published, the content is indexed and archived instantaneously and its underlying data exported to relevant specialised databases. Simultaneously, a suite of various metrics is enabled to facilitate tracking the usage of articles and sub-article elements, such as figures and tables.

“We have deeply enjoyed our collaboration with the Natural History Museum of Berlin for the past seven years that started with two great journals moving to our scholarly portfolio and advanced open access. Now, I am delighted to strengthen this wonderful partnership by welcoming Fossil Record and its fantastic editorial team to the families of ARPHA and Pensoft. I am certain that together we will not only repeat the success we had with DEZ and ZSE, but will actually build on it,”

says Prof. Dr Lyubomir Penev, founder and CEO at ARPHA and Pensoft.

About the Natural History Museum of Berlin:

The “Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science” is an integrated research museum within the Leibniz Association. It is one of the most important research institutions worldwide in the areas of biological and geological evolution and biodiversity.

The Museum’s mission is to discover and describe life and earth – with people, through dialogue. As an excellent research museum and innovative communication platform, it wants to engage with and influence the scientific and societal discourse about the future of our planet, worldwide. Its vision, strategy and structure make the museum an excellent research museum. The Natural History Museum of Berlin has research partners in Berlin, Germany and approximately 60 other countries. Over 700,000 visitors per year as well as steadily increasing participation in educational and other events show that the Museum has become an innovative communication centre that helps shape the scientific and social dialogue about the future of our earth.

Museum of New Zealand’s journal Tūhinga moves to Pensoft’s ARPHA Publishing Platform

Having decided to turn Tūhinga “into a 21st-century”, digital-native diamond open-access journal, the Museum of New Zealand Te Papa Tongarewa signed with scholarly publisher and technology provider Pensoft and its publishing platform ARPHA. As part of their agreement, not only is the journal to make its future content easy to read and discover by readers and computer algorithms, but will also do so for its legacy content.

Having decided to turn Tūhinga “into a 21st-century”, digital-native diamond open-access journal, the Museum of New Zealand Te Papa Tongarewa signed with scholarly publisher and technology provider Pensoft and its publishing platform ARPHA. As part of the agreement, not only is the journal to make its future content easy to read and discover by readers and computer algorithms, but will also do so for its legacy publications previously available solely in print. 

Tūhinga: Records of the Museum of New Zealand Te Papa Tongarewa is the successor of the Museum of New Zealand Records, the National Museum of New Zealand Records, and the Dominion Museum Records in Ethnology. Together, the outlets have acquired a nearly two century-worth of scientific knowledge provided by the museum’s curators, collection managers, and research associates across disciplines, from archaeology to zoology.

The renovated Tūhinga is to utilise the whole package of signature services provided by the platform, including ARPHA’s fast-track, end-to-end publishing system, which benefits readers, authors, reviewers and editors alike. 

This means that each submitted manuscript is to be carried through the review, editing, publication, dissemination and archiving stages without leaving the platform’s collaboration-centred online environment. The articles themselves are to be openly available in PDF, machine-readable JATS XML formats, and semantically enriched HTML for better reader experience. Thus, the journal’s articles will be as easy to discover, access, reuse and cite as possible. Once published, the content is to be indexed and archived instantaneously and its underlying data exported to relevant specialised databases. Simultaneously, a suite of various metrics is to be enabled to facilitate tracking the usage of articles and sub-article elements – like figures and tables – in real time.

The journal’s legacy content is to also become machine-discoverable and more user-friendly. Each of these papers will also be assigned with DOI and registered at CrossRef, while their metadata will be indexed at relevant databases. On the new journal website, they will be displayed as embedded PDF documents, while the reader will be able to do a full-text search of the article’s content.

Tūhinga welcomes original collections-based research in the natural sciences and humanities, including museological research, where its multidisciplinarity reflects the breadth and range of museum-based scholarship. The journal focuses primarily on New Zealand and the Pacific, but all contributions are considered. Having opted for a Diamond Open Access policy, the journal is to charge neither its readers, nor the authors.

“It’s a great honour to sign with the Museum of New Zealand Te Papa Tongarewa and provide our publishing services to Tūhinga. Particularly, we take pride in letting the whole wide world straight into the holdings of Te Papa and the knowledge they have prompted in the distant past: something that would not typically be possible had they remained only on paper,”

says Prof. Dr Lyubomir Penev, founder and CEO at ARPHA and Pensoft.

RIO Journal 5 years on: over 300 published outcomes from all around the research cycle

Five years on, the Open Science-driven journal Research Ideas and Outcomes (RIO) published an editorial that looks back on the 300 research ideas and research outcomes it has published so far.

Since its early days, RIO has enjoyed quite positive reactions from the open-minded academic community for its innovative approach to Open Science in practice: it provides a niche that had long been missing, namely the publication of early, intermediate and generally unconventional research outcomes from all around the research cycle (e.g. grant proposals, data management plans, project deliverables, reports, policy briefs, conference materials) in a cross-disciplinary scientific journal. In fact, several months after its launch, in 2016, the journal was acknowledged with the SPARC Innovator Award.

‘Alternative’ research publications

In times when posting a preprint was seen as a novel and rather bold practice across many fields, RIO facilitated much deeper dives into the research process, in order to unveil scientific knowledge and the process by which it is gathered, well before any final conclusions have been drawn. Long story short, to date, RIO has published 33 Research Ideas78 Grant Proposals16 Data Management Plans33 Workshop Reports and 5 PhD Project Plans, in addition to plenty of other early, interim and final non-traditional research outcomes, as well as conventional articles. Over time, RIO has kept adding additional article types to its list of publication types, with a few more expected in the near future.

What’s more, over the years, we’ve already observed how papers published in RIO successfully followed up on the continuity of the research process. For example, the Grant Proposal for the “Exploring the opportunities and challenges of implementing open research strategies within development institutions” project, funded by the International Development Research Centre (IDRC), was followed by the project’s Data Management Plan a year later.

Five years later, the figures reflecting the usage and engagement with the content published in RIO are evidently supportive of the value of having non-final and unconventional academic publications. For instance, the Grant Proposal for the COST Action DNAqua-Net, a still ongoing project dedicated to the development of novel genetic tools for bioassessment and monitoring of aquatic ecosystems, is the article with the most total views in RIO’s publication record to date. In the category of sub-article elements, whose usage is also tracked at the journal, the most viewed figure belongs to a Project Report and illustrates a sample code meant to be used in future neuroimaging studies. Similarly, the most viewed table ever published in RIO is part of a Workshop Report that summarises ASAPbio‘s third workshop, dedicated to the technical aspects of services related to the promotion of preprints in the biomedical and other life science communities.

Response to societal challenges

A unique and defining staple for RIO since the very beginning has also been the pronounced engagement with the Sustainable Development Goals (SDGs), as formulated by the United Nations right around the time of RIO’s launch. In order to highlight the societal impact of published research, RIO lets authors map their articles to the SDGs relevant to their paper. Once published, the article displays the associated badge(s) next to its title. Readers of the journal can even search RIO’s content by SDG, in the same way they would filter articles by subject, publication types, date or funding agency. Next on the list for RIO is to add another level of granularity to the SDGs mapping. The practice has already been piloted by mapping relevant RIO articles to the ten targets under SDG14 (Life below water).

Taking transparency, responsibility and collaboration in academia and scholarly publishing up another notch, RIO requires for reviews to be publicly available. In addition, the journal supports post-publication reviews, where peers are free to post their review anytime. In turn, RIO registers each review with its own DOI via CrossRef, in order to recognise the valuable input and let the reviewers easily refer to their contributions. A fine example is a Review Article exploring the biodiversity-related issues and challenges across Southeast Asia, which currently has a total of three public peer reviews, one of which is provided two years after the publication of the paper.

Public, transparent and perpetual peer review, pre- and/or post-publication

What’s more striking about peer review at RIO, however, is that it is not always mandatory. Given that the journal publishes many article types that have already been scrutinised by a legitimate authority – for instance, Grant Proposals that have previously been evaluated by a funder or defended PhD Theses – it only makes sense to avoid withholding these publications and duplicating associated evaluation efforts. On such occasions, all an author needs to do is provide a statement about the review status of their paper, which will be made public alongside the article.

On the other hand, where the article type of a manuscript requires pre-publication review, to avoid potential delays caused by the review process and editorial decisions, RIO encourages the authors to post their pre-review manuscript as a preprint on the recently launched ARPHA Preprints platform, subject to a quick editorial screening, which would only take a few days.

Further, RIO has now abandoned the practice of burdening the journal’s editors with the time-consuming task of finding reviewers, and instead requiring the submitting author to invite suitable reviewers upon submission, who are then immediately and automatically invited by the system. While significantly expediting the editorial work on a manuscript, this practice doesn’t compromise the quality of peer review in the slightest, since the reviews go public, while the final decision about the acceptance of the paper lies with the editor, who is also overlooking the process and able to intervene and invite additional reviewers anytime, if necessary.

Project-driven knowledge hub

The most significant novelty at RIO, however, is perhaps the newly assumed role of the journal as “a project-driven knowledge hub“, targeting specifically the needs of research projects, conference organisers and institutions. For them, RIO provides a one-stop source for the outputs of their scientists, in order to comply with the requirements of their funders or management, or simply to facilitate the discoverability, reusability and citability of their academic outputs and to highlight their interconnectedness.

Unlike typical permanent article collections, already widely used in scholarly publishing, with RIO, collection owners can take advantage of the unique opportunity to add a wide range of research outputs, including such published elsewhere, in order to provide even greater context to the assembled research outputs in their project- or institution-branded article collection (see the Horizon 2020 Project Path2Integrity‘s project collection as an example).

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

For example, a project coordinator could open a collection under the brand of the project, and start by publishing the Grant Proposal, followed shortly by Data and Software Management Plans and Workshop Reports. Thus, even at this early point in the project’s development, the funder – and with them everyone else – would already have strong evidence of the project’s dedication to transparency and active science communication. Later on, the project’s participants would all be able to easily add to the project’s collection by either submitting their diverse research outputs straight to RIO and having it accepted by the collection lead editor, or providing metadata and link to their publication from elsewhere, even preprints. If the document is published outside of RIO, its metadata, i.e. author names and affiliations, article title and publication date, show up in the collection, while a click on the item will lead to the original publication. As the project progresses, the team behind it could add more and more outputs (e.g. Project Reports, Guidelines and Policy Briefs), continuously updating the public and the relevant stakeholders about the development of their work. Eventually, the collection will be able to provide a comprehensive and fully transparent report of the project from start to finish.

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Senckenberg Nature Research Society transfers three journals to ARPHA Platform

Arthropod Systematics & Phylogeny, Vertebrate Zoology and Geologica Saxonica are the latest historic titles to select the various services and advanced technology provided by the OA-born scholarly publishing platform

One of the largest natural research associations in Germany, the Senckenberg Nature Research Society moved three of its international, open-access scholarly journals to the publishing platform ARPHA, following a recent contract with the scientific publisher and technology provider Pensoft.

Having opted for the white-label publishing solution, the journals remain under the brand of the Society and the Senckenberg Natural History Collections Dresden, one of the oldest natural-science museums in the world. Despite transitioning to a new platform, the past volumes of the journals remain accessible from a link on their website homepages.

Following their recent move to the Pensoft-developed publishing platform, Arthropod Systematics & PhylogenyVertebrate Zoology and Geologica Saxonica have not only acquired their own glossy and user-friendly websites, but have also taken advantage from ARPHA’s signature fast-track, end-to-end publishing system, which is to benefit all journal users: authors, reviewers and editors alike. In addition, the journals are already using many of the unique services offered by ARPHA, including publication in PDF, semantically enhanced HTML and machine-readable XML formats; advanced data publishing; sub-article-level usage metrics; automated export of sub-article elements and data to key aggregators; web-service integrations with major indexing and archiving databases; and others.

In particular, to the appeal of the authors, editors and reviewers, the ARPHA’s collaboration-centred online environment takes care after each submitted manuscript during the review, editing, publication, dissemination and archiving stages, so that no one needs to deal with locally stored files and their transfer by email or third-party cloud storages. Additionally, the platform is designed to regularly notify the users about any required action, thus sparing the burden of unnecessary communication and ensuring the speedy processing of manuscripts.

All three journals operate a Diamond Open Access policy, thanks to the support of the Senckenberg Nature Research Society, making the journals free to publish for all authors.

Arthropod Systematics & Phylogeny

Arthropod Systematics & Phylogeny is the successor of the historical Entomologische Abhandlungen, formerly published by the Museum of Zoology at Dresden.

Its scope covers the taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of arthropod taxa, but excludes faunistics and research with a strong regional focus. Descriptions of new taxa are only welcome when embedded in a wider context, for example, a phylogenetic, evolutionary, or biogeographical framework.

Currently, the journal enjoys an Impact Factor of 1.51 and a continuously increasing Scopus CiteScore.

Vertebrate Zoology

Similarly, Vertebrate Zoology was preceded by Zoologische Abhandlungen, also formerly published by the Museum of Zoology at Dresden. Its first publications since the move to ARPHA Platform and part of the first journal volume for 2021 are already a fact.

The journal deals with research on taxonomy, morphology, anatomy, phylogeny, historical biogeography and palaeontology of vertebrates. Again, descriptions of new taxa should be integrated into a proper context, for example, a complete revision of a taxon. To support accountability and reproducibility in science and academia, the journal requires that studied specimens have to be deposited in a public scientific collection.

Vertebrate Zoology’s Impact Factor is currently standing at 1.167, while its last Scopus CiteScore reached 2.1 (2019).

Geologica Saxonica

Geologica Saxonica – Journal of Central European Geology, began its life in distant 1876, when it was founded under the name Mitteilungen aus dem Königlichen Mineralogisch-Geologischen und Prähistorischen Museum by German geologist Hanns Bruno Geinitz, renowned for his work on the Carboniferous and Cretaceous rocks and fossils of Saxony.

The journal’s scope ecompasses geology, paleontology, stratigraphy, petrography, mineralogy and geoscience history with focus on Central Europe.

“At Pensoft, we are delighted to support a world-renowned natural history association like Senckenberg in carrying its legacy and treasure of knowledge into our days and well beyond. Now, with ARPHA’s white-label solution, we’re certain that the journals will simultaneously preserve their identity and enjoy all perks of modern and technologically advanced publishing,”

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

“We are very pleased to have found reliable partners in Pensoft and the ARPHA platform for our three publications to further increase their visibility. Senckenberg’s scientific publications have a long – almost 200-year tradition – and are now shown in a new and innovative design with unprecedented information retrieval options!”

says Prof. Dr. Uwe Fritz, Editor-in-Chief of the journal Vertebrate Zoology and head of the Department of Zoology at Senckenberg Natural History Collections in Dresden.

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Senckenberg is not the first prestigious German research institution to sign an agreement with Pensoft and ARPHA Platform. Since 2014, the Natural History Museum Berlin has trusted the publisher with its own historical titles in the Biology domain: Deutsche Entomologische Zeitschrift and Zoosystematics and Evolution. In 2017, Evolutionary Systematics by the University of Hamburg, another prominent journal with a legacy in the field of Zoology, followed suit. Last year, Zitteliana, a historical scholarly journal covering all fields of paleontology and geobiology by the State Natural History Collection of Bavaria (SNSB) also announced its joining the journal portfolio of Pensoft and ARPHA Platform.

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Making the most of conferences with modern publishing and indexing practices

Given scientific conferences present academics with the fantastic opportunity to meet up and discuss their latest work, as well as share their vision for the future of their field, it’s no wonder that, historically, the majority of ground-breaking science can easily be traced back to a particular event.

This said, don’t you think that we need to do everything within our powers to ensure the visibility, dissemination and long-term accessibility of research presented and linked to these wonderful drivers of scientific progress that conferences are? Similarly to the care conference organisers take to make sure the event runs smoothly and the attendants are happy with the programme and enjoy themselves, the organisational committee should also be thinking how to preserve all those promising pieces of research well after the event is over.

Here at Pensoft, an open-access scholarly publisher, founded by scientists, we’ve been contemplating for a while now how to encourage and support the community to efficiently open up the valuable outputs to researchers and readers well beyond the publication of abstracts in an abstract book of the conference. 

As a result, we came up with several simple, yet efficient publishing solutions for scientific conferences to collect and contextualise various research outputs either presented at or resulting from the event.

Bear in mind that with any solution, all publications enjoy the benefits seen in conventional research papers, such as:

  • Crossref registration and individual DOI to ensure preservation;
  • Publication in PDF, semantically enhanced HTML and data-minable XML formats to improve readability, accessibility and findability;
  • Indexing and archiving at multiple, industry leading databases to increase visibility;
  • PR and social media promotion to boost outreach to various audiences.

Collections of conference abstracts, posters and presentations

Conference (video) abstracts, posters and presentations are easily the first to fall victims of the ephemerality of an event, yet these are too often the stepping stones to major scientific discoveries. This is why a few years back we launched ARPHA Conference Abstracts (ACA), where conference organisers can open their own collection and provide the participants with submission, review and publication of their abstracts ahead of the conference.

Furthermore, these abstracts can be handled editorially in sub-collections, e.g. the convenors of symposia or working groups within a conference will take care of the abstracts submitted to them, thus spreading the editorial workload across larger teams of editors and organisers.

Not only will conference organisers spare themselves the worries about providing a special platform for abstracts submissions, but this will also facilitate presenting authors, who will be able to easily point to their contribution before, during or after their presentations. On the contrary, the abstracts are assigned with DOIs, published in human-readable PDF and HTML and machine-actionable JATS XML, permanently preserved on ARPHA and Zenodo, and easy to find, access and cite, just like a conventional research paper, providing authors with full credit for their work early on.

Further, with ACA, the conference abstracts can be enhanced into what we call “extended abstracts”, meaning they can also include data, images, videos and multimedia. After the conferences, we can add video recordings of the presentations or graphic files of posters, so that these are visualised on the page of each abstract.

For example, take a look at the conference abstract collection of the Vth International Congress on Biodiversity: “Taxonomy, Speciation and Euro-Mediterranean Biodiversity”.

Conference proceedings

About the time we launched ACA, we also created ARPHA Proceedings, in order to also find a place for full-text conference papers. Similarly, the platform supports dedicated collections, where conference attendants are invited to submit and publish dynamically articles under the imprint of the event.

Conference papers in ARPHA Proceedings can also include data, figures and citations, and can also be updated with video recordings, posters and presentations following the conference.

Check out an example by the VI International Forum on Teacher Education.

Article topical collections and special issues resulting from conferences

Naturally, papers resulting from a particular conference are contextually linked, so a one-stop place to discover topical studies sharing one and the same topic would be greatly appreciated by readers and future researchers. In turn, this would lead to better viewership and citability of the papers in the collection.

With our user-friendly, dedicated workflow for special issues and permanent topical article collections, we’ve made it easy for guest editors across our journals to pitch and manage article collections, in order to bring together valuable and related studies. Using such a collection under the theme of your conference in a suitable journal, you can invite your conference’s participants or, better yet, all scientists working within the field, to submit their work in a nice package of topical science. We’d be happy to assist you with the identification of the most suitable journal for your conference, authors and goals.

See an example from One Ecosystem and the collection “Mapping and assessment of ecosystem condition and ecosystem services across different scales and domains in Europe”, the result from the “Mapping and assessment of ecosystem services – Science in action” conference, held in 2017.

Bringing together traditional and non-conventional research outputs, (e.g. research ideas, grant proposals, conference materials or workshop reports) with RIO Journal’s article collections

Undoubtedly, valuable research outcomes come in many shapes and sizes well beyond research papers, conference abstracts, posters and proceedings. We are firm supporters that every research item, even early and interim outputs, could be of value to the scientist next in line within a particular study.

This is why we launched the award-winning journal Research Ideas and Outcomes (RIO), where your collections can include both conventional and non-traditional research outputs, such as research ideas, posters, workshop reports, forum papers, policy briefs, software and data management plans to name a few. Furthermore, in RIO, you can even link articles or preprints published elsewhere to your collection via their metadata. Similarly to other Pensoft journals, in RIO, you will have the full control to whom you are opening your collection for submissions, allowing you to either limit it to the outcomes coming from your conference or welcome submissions from other researchers as well.

A permanent topical collection in RIO Journal may include a diverse range of both traditional and unconventional research outputs, as well as links to publications from outside the journal (see What can I publish on the journal’s website). 

See the Brainhack 2016 Project Reports, whose aim is to collate reports from the 2016 Brainhack events. Also, check out the collection of the European Biodiversity Observation Network (EU BON) Project, providing a nice example for a wide range of publication types.

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Don’t hesitate to get in touch to discuss your own case and select the best option for your conference – we’ll be happy to hear from you!

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Italian Society of Vegetation Science signs with Pensoft to publish its journal on ARPHA

The first 2020 papers of the open-access, peer-reviewed international journal Plant Sociology are now available on the journal’s new, user-friendly and visually appealing website

Having succeeded the historical journals of the Italian Society of Vegetation Science (Società Italiana di Scienza della Vegetazione): Fitosociologia (1990-2011) and Notiziario della Societa Italiana di Fitosociologia (1964-1989), the open-access, peer-reviewed international journal Plant Sociology undergoes another major transformation by moving to the technologically advanced ARPHA Platform, after signing with the scholarly publisher and technology provider Pensoft.

As a result of the recently started partnership, the first 2020 papers of Plant Sociology are now available on the journal’s new website. All pre-2020 issues remain available on the former website.

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.

Amongst the first newly published papers is an article by a team from the University of L’Aquila, which reports on two years of observations of the vegetation dynamics at the Gran Sasso – Monti della Laga National Park in central Italy, after the protected area suffered from an accidental fire of anthropogenic origin in 2017. With their study, the researchers aim to determine the potential of the Sentinel-2 satellite as a tool to measure, identify and monitor the short-term response of vegetation in a peculiar mountainous landscape.

Another new publication presents a phytosociological survey on the weed vegetation of two crops of Protected Designation of Origin: the bean “Fagiolo Cannellino di Atina” and the red pepper “Peperone di Pontecorvo” – both growing exclusively within a few hundreds of square kilometres in the Province of Frosinone (central Italy), conducted at four selected farms by researchers at the Sapienza University of Rome.

Thanks to the Pensoft’s signature open-access scholarly publishing platform ARPHA, Plant Sociology 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 from 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.

Plant Sociology has a completely renewed Editorial board, which sees Daniela Gigante from the University of Perugia in the role of Editor-in-Chief, and Simonetta Bagella (University of Sassari), Gianni Bacchetta (University of Cagliari) and Daniele Viciani (University of Florence) as Co-editors. The Editorial board is complemented by a Consultant editor and an Editorial secretary (respectively, Edoardo Biondi and Diana Galdenzi, both from the Polytechnic University of Marche, Ancona). A large, international Editorial team includes 35 members with specific skills and long-dated expertise in various fields related to vegetation science. A dedicated Social media team takes care of the dissemination of the journal.

“At the Plant Sociology‘s Editorial board, we are looking with great expectations to the cooperation with Pensoft, certain that the publisher’s skills and experience will support the journal in its growth and consolidation as an international reference point for vegetation science studies,”

says Editor-in-Chief Dr Daniela Gigante.

“It’s delightful to have the Italian Society of Vegetation Science putting their trust in us with their signature journal. With our strong background in scholarly publishing, technology development and open science practices, I am certain that we are to provide the right venue for a high-quality and enterprising journal like Plant Sociology,”

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

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Follow Plant Sociology 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.

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

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

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

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

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

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

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

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

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

Heritage, Memory and Conflict Journal (HMC)

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

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

Journal of European Landscapes (JEL) 

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

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

Vegetation Classification and Survey (VCS)

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

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

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

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

Plant Sociology 

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

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

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

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

Caucasiana

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

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

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

The EASE Journal: European Science Editing (ESE)

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

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

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

Bulgarian Journal of Cardiology

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

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

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