“Not only does it mean that content is persistent in merit and quality, but that innovative research outputs are already appreciated within academia,” says Editor-in-Chief Prof Dr Benjamin Burkhard
Seven years after its official launch in May 2016, the One Ecosystem journal has successfully completed the rigorous quality and integrity assessment at Web of Science.
The news means that One Ecosystem might see its very first Journal Impact Factor (JIF) as early as 2024, following the latest revision of the metric’s policies Clarivate announced last July. According to the update, all journals from the Web of Science Core Collection are now featured in the Journal Citation Reports, and thereby eligible for a JIF.
“Giving all quality journals a Journal Impact Factor will provide full transparency to articles and citations that have contributed to impact, and therefore will help them demonstrate their value to the research community. This decision is aligned to our position that publications in all quality journals, not just highly cited journals, should be eligible for inclusion in research assessment exercises,” said back then Dr Nandita Quaderi, Editor-in-Chief and Editorial Vice President at Web of Science.
“We are happy to learn that Web of Science has recognised the value and integrity of One Ecosystem in the scholarly landscape. Not only does it mean that the scientific content One Ecosystem has been publishing over the years is persistent in merit and quality, but that innovative research outputs are already widely accepted and appreciated within academia.
After all, one of the reasons why we launched One Ecosystem and why it has grown to be particularly distinguished in the field of ecology and sustainability is that it provides a scholarly publication venue for traditional research papers, as well as ‘unconventional’ scientific contributions,”
“These ‘unconventional’ research outputs – like software descriptions, ecosystem inventories, ecosystem service mappings and monitoring schema – do not normally see the light of day, let alone the formal publication and efficient visibility. We believe that these outputs can be very useful to researchers, as well as practitioners and public bodies in charge of, for example, setting up indicator frameworks for environmental reporting,”
“In fact, last year, we also launched a new article type: the Ecosystem Accounting table, which follows the standards set by the the System of Environmental-Economic Accounting Ecosystem Accounting (SEEA EA). This publication type provides scientists and statisticians with a platform to publish newly compiled accounting tables,”
Previously, One Ecosystem has been accepted for indexing at over 60 major academic databases, including Scopus, DOAJ, Cabell’s Directory, CABI and ERIH PLUS. In June 2022, the journal received a Scopus CiteScore reading 7.0, which placed it in Q1 in five categories: Earth and Planetary Sciences; Ecology; Nature and Landscape Conservation; Agricultural and Biological Sciences (miscellaneous); Ecology, Evolution, Behavior and Systematics.
Welcomed are taxonomic and other biodiversity-related research articles, which demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data
The EU-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) will support free of charge publications*submitted to the dedicated topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach” in the Biodiversity Data Journal, demonstrating advanced publishing methods of linked biodiversity data, so that they can be easily harvested, distributed and re-used to generate new knowledge.
BiCIKL is dedicated to building a new community of key research infrastructures, researchers and citizen scientists by using linked FAIR biodiversity data at all stages of the research lifecycle, from specimens through sequencing, imaging, identification of taxa, etc. to final publication in novel, re-usable, human-readable and machine-interpretable scholarly articles.
Achieving a culture change in how biodiversity data are being identified, linked, integrated and re-used is the mission of the BiCIKL consortium. By doing so, BiCIKL is to help increase the transparency, trustworthiness and efficiency of the entire research ecosystem.
The new article collection welcomes taxonomic and other biodiversity-related research articles, data papers, software descriptions,and methodological/theoretical papers. These should demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.
To be eligible for the collection, a manuscript must comply with one or more of the conditions listed below. In the submission form, the author will need to mention the condition(s) applicable to the manuscript as an Author’s note to the editor.
All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics.
Conditions for publication in the article collection:
The authors are expected to use explicit Globally Unique Persistent and Resolvable Identifiers (GUPRI) or other persistent identifiers (PIDs), where such are available, for the different types of data they use and/or cite in the manuscripts (specimens IDs, sequence accession numbers, taxon name and taxon treatment IDs, image IDs, etc.)
Global taxon reviews in the form of “cyber-catalogues” are welcome if they contain links of the key data elements (specimens, sequences, taxon treatments, images, literature references, etc.) to their respective records in external repositories. Taxon names in the text should not be hyperlinked. Instead, under each taxon name in the catalogue, the authors should add external links to, for example, Catalogue of Life, nomenclators (e.g. IPNI, MycoBank, Index Fungorum, ZooBank), taxon treatments in Plazi’s TreatmentBank or other relevant trusted resources.
Taxonomic papers (e.g. descriptions of new species or revisions) must contain persistent identifiers for the holotype, paratypes and at least most of the specimens used in the study.
Specimen records that are used for new taxon descriptions or taxonomic revisions and are associated with a particular Barcode Identification Number (BIN) or Species Hypothesis (SH) should be imported directly from BOLD or PlutoF, respectively, via the ARPHA Writing Tool data-import plugin.
More generally, individual specimen records used for various purposes in taxonomic descriptions and inventories should be imported directly into the manuscript from GBIF, iDigBio, or BOLD via the ARPHA Writing Tool data-import plugin.
In-text citations of taxon treatments from Plazi’s TreatmentBank are highly welcome in any taxonomic revision or catalogue. The in-text citations should be hyperlinked to the original treatment data at TreatmentBank.
Hyperlinking other terms of importance in the article text to their original external data sources or external vocabularies is encouraged.
Tables that list gene accession numbers, specimens and taxon names, should conform to the Biodiversity Data Journal’s linked data tables guidelines.
Theoretical or methodological papers on linking FAIR biodiversity data are eligible for the BiCIKL collection if they provide real examples and use cases.
Data papers or software descriptions are eligible if they use linked data from the BiCIKL’s partnering research infrastructures, or describe tools and services that facilitate access to and linking between FAIR biodiversity data.
Articles that contain nanopublications created or added during the authoring process in Biodiversity Data Journal. A nanopublication is a scientifically meaningful assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, for example biotic relationship between taxa, or habitat preference of a taxon. The in-built workflow ensures the linkage and its persistence, while the information is simultaneously human-readable and machine-interpretable.
Manuscripts that contain or describe any other novel idea or feature related to linked or semantically enhanced biodiversity data will be considered too.
We recommend authors to get acquainted with these two papers before they decide to submit a manuscript to the collection:
Here are several examples of research questions that might be explored using semantically enriched and linked biodiversity data:
(1) How does linking taxon names or Operational Taxonomic Units (OTUs) to related external data (e.g. specimen records, sequences, distributions, ecological & bionomic traits, images) contribute to a better understanding of the functions and regional/local processes within faunas/floras/mycotas or biotic communities?
(2) How could the production and publication of taxon descriptions and inventories – including those based mostly on genomic and barcoding data – be streamlined?
(3) How could general conclusions, assertions and citations in biodiversity articles be expressed in formal, machine-actionable language, either to update prior work or express new facts (e.g. via nanopublications)?
(4) How could research data and narratives be re-used to support more extensive and data-rich studies?
(5) Are there other taxon- or topic-specific research questions that would benefit from richer, semantically enhanced FAIR biodiversity data?
Once published, specimen records data are being exported in Darwin Core Archive to GBIF.
The data and taxon treatments are also exported to several additional data aggregators, such as TreatmentBank, the Biodiversity Literature Repository, and SiBILS amongst others. The full-text articles are also converted to Linked Open Data indexed in the OpenBiodiv Knowledge Graph.
All articles will need to acknowledge the BiCIKL project, Grant No 101007492 in the Acknowledgements section.
* The publication fee (APC) is waived for standard-sized manuscripts (up to 40,000 characters, including spaces) normally charged by BDJ at € 650. Authors of larger manuscripts will need to cover the surplus charge (€10 for each 1,000 characters above 40,000). See more about the APC policy at Biodiversity Data Journal, or contact the journal editorial team at: bdj@pensoft.net.
Follow the BiCIKL Project on Twitter and Facebook.Join the conservation on via #BiCIKL_H2020.
You can also follow Biodiversity Data Journal on Twitter and Facebook.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.
OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System.
As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.
In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.
“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”
he adds.
At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.
Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL.
As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions.
Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.
Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.
On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.
“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”
All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research.
As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.
The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service.
According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.
While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals.
This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.
“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”
said Robert Kiley, Head of Strategy at cOAlition S.
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About cOAlition S:
On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.
About Plan S:
Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.
By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.
This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.
All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.
“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”
comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.
“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”
adds Yvonne Campfens, Executive Director of the OA Switchboard.
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About the OA Switchboard:
A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.
About Pensoft:
Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.
All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.
On this occasion full of sweet memories, we are also inviting you to complete this 3-minute survey. We would deeply appreciate your invaluable feedback!
It was in late 1992 when biologist and ecologist Prof Dr Lyubomir Penev in a collaboration with his friend Prof. Sergei Golovatch established Pensoft: a scholarly publisher with the ambition to contribute to novel and even revolutionary methods in academic publishing by applying its own approach to how science is published, shared and used. Inspired by the world’s best practices in the field, Pensoft would never cease to view the issues and gaps in scholarly publishing in line with its slogan: “by scientists, for scientists”.
As we celebrate the 30th anniversary of Pensoft, we are asking ourselves: What’s a tree without its roots?
That’s why we’ve put up an attractive timeline of Pensoft’s milestones on our website, and complemented it with some key figures, in an attempt to translate those years into numbers. Yet, one can say only that much in figures. Below, we’ll give a bit more context and background about Pensoft’s key milestones.
1994: Pensoft publishes its first book & book series
In time for New Year’s Day in 1994, we published the first book bearing the name of Pensoft. The catalogue of the sheet weaver spiders (Lyniphiidae) of Northern Asia did not only set the beginning of the publishing activities of Pensoft, but also started the extensive Pensoft Series Faunistica, which continues to this day, and currently counts over 120 titles.
2003: Pensoft joins its first EU-funded research project
By 2003, we were well-decided to expand our activities toward participation in collaborative, multinational projects, thereby building on our mission to shed light and communicate the latest scientific work done.
By participating in the FP6-funded project ALARM (abbreviation for Assessing LArge-scale environmental Risks with tested Methods), coordinated by Dr. Joseph Settele from the Helmholtz Centre for Environmental Research (Germany), we would start contributing to the making of science itself in close collaboration with another 67 institutions from across Europe. Our role at ALARM during the five years of the duration of the project was to disseminate and communicate the project outcome. At the end of the project, we also produced the highly appreciated within the community Atlas of Biodiversity Risk.
As for today, 19 years later, Pensoft has taken part in 40 research projects as a provider of various services ranging from data & knowledge management and next-generation open access publishing; to communication, dissemination and (web)design; to stakeholder engagement; consultations; and event and project management.
Our project activities culminated last year, when we became the coordinator of a large and exciting BiCIKL project, dedicated to access to and linking of biodiversity data along the entire data and research life cycle.
2008: Pensoft launches its first scholarly journal to revolutionise & accelerate biodiversity research
Openly accessible and digital-first since the very start, the ZooKeys journal was born on a sunny morning in California during the Entomological Society of America meeting in 2007, when Prof Lyubomir Penev and his renowned colleague Dr Terry Erwin from the Smithsonian Institution agreed over breakfast that zoologists from around the world could indeed use a new-age taxonomic journal. What the community at the time was missing was a scholarly outlet that would not only present a smooth fast track for their research papers, while abiding by the highest and most novel standards in the field, but do so freely and openly to any reader at any time and in any place. Fast forward to 2021, ZooKeys remains the most prolific open-access journal in zoology.
With over 1,100 volumes published to date, ZooKeys is one of our most renowned journals with its own curious and intriguing history. You can find more about it in the celebratory blog post we published on the occasion of the journal’s 1,000th volume in late 2020.
At the time of writing, Pensoft has 21 journals under its own belt, co-publishes another 16, and provides its self-developed journal management platform ARPHA to another 35 scholarly outlets.
2010a: Pensoft launches its first journal publishing platform
By 2010, we realised that the main hurdle holding our progress as a next-age publisher of scientific knowledge was posed by the technology – or lack thereof – underlying the publishing process. We figured that – in our position of users – we were best equipped to figure what exactly this backbone structure should be made of.
This is when we released the publishing platform TRIADA, which was able to support both the editorial and the publication processes at our journals. This was also the point in time when we added “technology provider” to the Pensoft’s byline. Surely, we had so many ideas in our mind and TRIADA was only the beginning!
2010b: In the 50th issue of ZooKeys, Pensoft publishes the first semantically enhanced biodiversity research papers
Later the same year, TRIADA let us write some history. The 50th volume of ZooKeys wasn’t only special because of its number. It contained the first scholarly papers in the study of biodiversity featuring semantic enrichments.
The novelty that keeps a taxon only a click away from a list of related data, including its occurrences, genomics data, treatments, literature etc. is a feature that remains a favourite to our journals’ users to this very day. Unique to date, this workflow is one of the many outcomes of our fantastic long-time collaboration and friendship with Plazi.
2011: Journal of Hymenoptera Research becomes the first society journal to move to Pensoft
Three years after the launch of the very first Pensoft journal, we received a request from the International Society of Hymenopterists who wanted for their own journal: the Journal of Hymenoptera Research to follow the example of ZooKeys and provide to their authors, editors and readers a similar set of services and features designed to streamline biodiversity knowledge in a modern, user-friendly and highly efficient manner.
Ever since, the journal has been co-published by the Society and Pensoft, and enjoyed growing popularity and appeal amongst hymenopterists from around the world.
Impact Factor and CiteScore trend for Journal of Hymenoptera Research since 2015.
2013: Pensoft replaces TRIADA with its own in-house built innovative ARPHA Platform
As we said, TRIADA was merely the crude foundation of what was to become the ARPHA publishing platform: a publishing solution providing a lot more than an end-to-end entirely online environment to support the whole publishing process on both journal and article level.
On top of that, ARPHA’s publishing package includes a variety of automated and manually provided services, web service integrations and highly customisable features. With all of those, we aimed at one thing only: create a comprehensive scholarly publishing solution to our own dearest journals and all their users.
Having just unveiled ARPHA Platform, we were quite confident that we have developed a pretty all-in publishing solution. Our journals would be launched, set up, hosted and upgraded safely under our watchful eye, while authors, editors and reviewers would need to send not a single email or a file outside of our collaborative environment from the moment they submit a manuscript to the moment they see it published, indexed and archived at all relevant databases.
Yet, we could still spot a gap left to bridge. The Pensoft Writing Tool (or what is now known as the ARPHA Writing Tool or AWT) provides a space where researchers can do the authoring itself prior to submitting a manuscript straight to the journal. It all happens within the tool, with co-authors, external collaborators, reviewers and editors all able to contribute to the same manuscript file. Due to the XML technology underlying AWT, various data(sets) and references can be easily imported in a few clicks, while a list of templates and content management features lets researchers spend their time and efforts on their scientific work rather than format requirements.
2015: Pensoft launches the open-science RIO Journal
Six years ago, amid heated discussions over the pros and cons of releasing scientific knowledge freely to all, we felt it’s time to push the boundaries even further.
No wonder that, at the time, a scholarly journal with the aim to bring to light ‘alternative’ research outputs from along the whole research process, such as grant proposals, project and workshop reports, data management plans and research ideas amongst many others, was seen as quite brave and revolutionary. Long story short, a year after its launch, RIO earned the honorary recognition from the Scholarly Publishing and Academic Resources Coalition (SPARC) to be named an Open Science Innovator.
Learn about the key milestones and achievements at RIO Journal to date – in addition to its future goals – in the special blog post and the editorial published on the occasion of the journal’s fifth anniversary.
2016: Pensoft provides ARPHA Platform as a white-label journal publishing solution for the first time
Led by our intrinsic understanding for scholars and smaller publishers, we saw the need of many journals and their owners to simultaneously secure a user-friendly and sustainable publishing solution for their scientific outlets. This is why we decided to also offer our ARPHA Platform as a standalone package of technology, services and features, dissociated with Pensoft as a publisher. This option is particularly useful for university presses, learned societies and institutions who would rather stick to exclusivity when it comes to their journal’s branding and imprint.
Another step forward to encompassing the whole spectrum of research outputs was to take care after conference materials: proceedings and abstracts. Once again, our thinking was that all scientific work and efforts need to be made openly available, accessible, reusable and creditable.
Both ARPHA Conference Abstracts and ARPHA Proceedings allow for organisers to conveniently bring the publications together in a conference-branded collection, thereby providing a one-stop permanent access point to all content submitted and presented at a particular event, alongside associated data, images, videos and multimedia, video recordings of conference talks or graphic files of poster presentations.
Publications at both platforms benefit from all key advantages available to conventional research papers at a Pensoft journal, such as registration at Crossref and individual DOI; publication in PDF, semantically enhanced HTML and data-minable XML formats; indexing and archiving at multiple major databases; science communications services.
2019: Pensoft develops the OpenBiodiv Knowledge Graph
As firm believers in the power and future of linked and FAIR data, at Pensoft we realise there is still a great gap in the way biodiversity data is collated, stored, accessed and made available to researchers and key stakeholders for further reuse.
In fact, this is an area within biodiversity research that is in dire need of a revolutionary mechanism to provide a readily available and convenient hub that allows a researcher to access all related data via multi-directional links interconnecting various and standardised databases, in accordance with the Web 2.0 principles.
As the first step in that direction, in 2019, we launched the OpenBiodiv Knowledge Graph, which began to collate various types of biodiversity data as extracted from semantically enhanced articles published by Pensoft and taxonomic treatments harvested by Plazi.
Since then, the OpenBiodiv Knowledge Graph has evolved into the Open Biodiversity Knowledgement Management System (OBKMS), which also comprises a Linked Open Dataset, an ontology and а website. Our work on the OBKMS continues to this day, fueled by just as much enthusiasm as in those early days in 2019.
By 2020, a number of factors and issues that had long persisted within scholarly publishing and academia had already triggered the emergence of multiple preprint servers. Yet, the onset of the unprecedented for our age COVID-19 pandemic, seemed like the final straw that made everyone realise we needed to start uncovering early scientific work, and we needed to do that fast.
At the time, we had already been considering applying the Pensoft approach to preprints. So, we came up with a solution that could seamlessly blend into our existing infrastructure.
Offered as an opt-in service to journals published on the ARPHA Platform, ARPHA Preprints allows for authors to check a box and post their manuscripts as a preprint as they are filling in the submission form at a participating journal.
Learn more about ARPHA Preprints on the ARPHA blog.
2021a: RIO Journal expands into a project-driven knowledge hub
Ever since its launch, RIO had been devised as the ultimate scholarly venue to share the early, intermediate and final results of a research project. While collections at the journal had already been put in good use, we still had what to add, so that we could provide a one-stop place for consortia to permanently store their outputs and make them easily discoverable and accessible long after their project had concluded.
With the upgraded collections, their owners received the oppotunity to also add various research publications – including scholarly articles published elsewhere, author-formatted documents and preprints. In the former case, the article is visualised within the collection at RIO via a link to its original source, while in the latter, it is submitted and published via ARPHA Preprints.
Over the years, we have been partnering with many like-minded innovators and their institutions from across the natural science community. Surely, we hadn’t successfully developed all those technologies and workflows without their invaluable feedback and collaborations.
In 2021, our shared passion and vision about the future of research data availability and usage culminated in the project BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library), which was granted funding by the European Commission and will run until April 2024.
Within BiCIKL, our team of 14 European institutions are deploying and improving our own and partnering infrastructures to bridge gaps between each other’s biodiversity data types and classes with the ultimate goal to provide flawless access to data across all stages of the research cycle. By the end of the project, together we will have created the first-of-its-kind Biodiversity Knowledge Hub, where a researcher will be able to retrieve a full set of linked and open biodiversity data.
Naturally, being a coordinator of such a huge endeavour towards revolutionising biodiversity science is a great honour by itself.
For us, though, this project has a special place in our hearts, as it perfectly resonates with the very reason why we are here: publishing and sharing science in the most efficient and user-friendly manner.
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.
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.
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
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.
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.
Herpetozoa, the peer-reviewed scientific journal of the Austrian Herpetological Society, renewed its contract with Pensoft, re-signing with the scholarly publisher for another five years. Published since 1988, the journal offers a venue for research articles, short contributions and reviews dealing with all aspects of the study of amphibians and reptiles.
Herpetozoa, thepeer-reviewed scientific journal of the Austrian Herpetological Society, renewed its contract with Pensoft, re-signing with the scholarly publisher for another five years. Published since 1988, the journal offers a venue for research articles, short contributions and reviews dealing with all aspects of the study of amphibians and reptiles.
Enticed by the opportunities that open access publishing offers, and looking to improve its visibility, Herpetozoa first came to Pensoft in 2019. The move equipped the journal with abrand new website and a full suite of publishing services tailored to the needs of biodiversity-themed academic publications available from ARPHA, Pensoft’s self-developed publishing platform.
In ARPHA’s fast-track publishing system, each manuscript is carried through all stages, from submission and reviewing to dissemination and archiving, without ever leaving the platform’s collaboration-friendly online environment. In addition, semantic enhancements, automated data export to aggregators, web-service integrations with major indexing databases, and a variety of publishing formats ensure that all articles are easy to find, access, and use by both humans and machines.
The journal also makes use of ARPHA Preprints, another service developed by Pensoft to streamline public access to the latest scientific findings. The platform allows authors to submit a preprint in a matter of seconds along with their manuscript, with no need to upload any additional files. Following a quick in-house screening, the preprint is then made available on ARPHA Preprints in a few days’ time. Once the associated paper is published, a two-way link between the article and the preprint is established via CrossRef.
In the past three years, we saw Herpetozoa publish some quite peculiar discoveries that were quick to attract the attention of the global media. Such was the case of a set of first-of-their-kind observations of kukri snakes gutting toads and eating their organs while still alive. At the same time, the journal doesn’t fail to bring public attention to urgent conservation and biodiversity loss issues like reptile poaching in Pakistan, as well as innovative methods to monitor delicate amphibians in a non-invasive manner.
