Tag: scientific

Here’s to a year of growing and succeeding together!

Within and beyond our Pensoft team, we celebrate a year of well-nourished partnerships and excitement for the future

Yet another hectic year has passed for our team at Pensoft, so it feels right to look back at the highlights from the last 12 months, as we buckle up for the leaps and strides in 2025.

In the past, we have used the occasion to take you back to the best moments of our most popular journals (see this list of 2023 highlights from ZooKeys, MycoKeys, PhytoKeys and more!); share milestones related to our ARPHA publishing platform (see the new journals, integrations and features from 2023); or let you reminisce about the coolest research published across our journals during the year (check out our Top 10 new species from 2021).

In 2022, when we celebrated our 30th anniversary on the academic scene, we extended our festive spirit throughout the year as we dived deep into those fantastic three decades. We put up Pensoft’s timeline and finished the year with a New Species Showdown tournament, where our followers on (what was back then) Twitter voted twice a week for their favourite species EVER described on the pages of our taxonomic journals.

Spoiler alert: we will be releasing our 2024 Top 10 New Species on Monday, 23 December, so you’d better go to the right of this screen and subscribe to our blog!

As we realised we might’ve been a bit biased towards our publishing activities over the years, this time, hereby, we chose to present you a retrospection that captures our best 2024 moments from across the departments, and shed light on how the publishing, technology and project communication endeavours fit together to make Pensoft what it is.

In truth, we take pride in being an exponentially growing family of multiple departments that currently comprises over 60 full-time employees and about a dozen freelancers working from all corners of the world, including Australia, Canada, Belgium and the United Kingdom. Together, we are all determined to make sure we continuously improve our service to all who have trusted us: authors, reviewers, editors, client journals, learned societies, research institutions, project consortia and other external collaborators.


After all, great deeds are only possible when you team up with great like-minded people!

Pensoft as an open-access academic publisher 

Pensoft’s stand at the 2024 TDWG-SPNHC joint conference (September, Japan).

In 2024, at Pensoft, we were hugely pleased to see a significant growth in the published output at almost all our journals, including record-breaking numbers in both submissions and publications at flagship titles of ours, including the Biodiversity Data Journal, PhytoKeys and MycoKeys. 

Other fantastic news came in June from our Indexing team, who confirmed that One Ecosystem: a quite unique and novel academic outlet we launched in collaboration with the Ecosystem Services Partnership in 2016 – received its first Impact Factor. 

Later in 2024, our colleagues, who work together with our clients to ensure their journals comply with the requirements of the top scholarly databases before they apply for indexation, informed us that another two journals in our portfolio have had their applications to Clarivate’s Web of Science successfully accepted. These are the newest journal of the International Association of Vegetation Science: Vegetation and Classification, and Metabarcoding and Metagenomics: a journal we launched in 2017 in collaboration with a team of brilliant scientists working together at the time within the DNAquaNet COST Action.

In 2024, we also joined the celebrations of our long-time partners at the Museum für Naturkunde Berlin, whose three journals: Zoosystematics and Evolution, Deutsche Entomologische Zeitschrift and Fossil Record are all part of our journal portfolio. This year marked the 10th Open Access anniversary of the three journals.

10 years of Open Access: Museum für Naturkunde Berlin and Pensoft celebrate a decade of partnership

In the meantime, we also registered a record in new titles either joining the Pensoft portfolio or opting for ARPHA Platform’s white-label publishing solution, where journal owners retain exclusivity for the publication of their titles, yet use ARPHA’s end-to-end technology and as many human-provided services as necessary.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev with Prof. Dr. Marc Stadler, Editor-in-Chief of IMA Fungus and President of the International Mycological Association at the Pensoft booth at the 12th International Mycological Congress (August, the Netherlands). 

Amongst our new partners are the International Mycological Association who moved their official journal IMA Fungus to ARPHA Platform. As part of Pensoft’s scholarly portfolio, the renowned journal joins another well-known academic title in the field of mycology: MycoKeys, which was launched by Pensoft in 2011. The big announcement was aptly made public at this year’s 12th International Mycological Congress where visitors of the Pensoft stand could often spot newly elected IMA President and IMA Fungus Chief editor: Marc Stadler chatting with our founder and CEO Lyubomir Penev by the Pensoft/MycoKeys booth.

Other partners who chose the services of ARPHA Platform for their journals in 2024 include the International Biogeography Society, United Arab Emirates University and Medical University Pleven.

On our end, we did not stop supporting enthusiastic and proactive scientists in their attempt to bridge gaps in scientific knowledge. In January, we launched the Estuarine Management and Technologies journal together with Dr. Soufiane Haddout of the Ibn Tofail University, Morocco. 

Later on, Dr. Franco Andreone (Museo Regionale di Scienze Naturali, Italy) sought us with the idea to launch a journal addressing the role of natural history museums and herbaria collections in scientific progress. This collaboration resulted in the Natural History Collections and Museomics journal, officially announced at the joint TDWG-SPNHC conference in Okinawa, Japan in August.

Natural History Collections and Museomics launches with its inaugural editorial

Around this time, we finalised our similarly exciting journal project in partnership with Prof. Dr. Volker Grimm (UFZ, Germany), Prof. Dr. Karin Frank (UFZ, Germany), Prof. Dr. Mark E. Hauber (City University of New York) and Prof. Dr. Florian Jeltsch (University of Potsdam, Germany). The outcome of this collaboration is called Individual-based Ecology: a journal that aims to promote an individual-based perspective in ecology, as it closes the knowledge gap between individual-level responses and broader ecological patterns.

ARPHA Platform welcomes new journal launched by Pensoft: Individual-based Ecology

The three newly-launched journals are all published under the Diamond Open Access model, where neither access, nor publication is subject to charges.

As you can see, we have a lot to be proud of in terms of our journals. This is also why in 2024 our team took a record number of trips to attend major scientific events, where we got the chance to meet face-to-face with long-time editors, authors, reviewers and readers of our journals. Even more exciting was meeting the new faces of scientific research and learning about their own take on scholarship and academic journals.

Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev welcomed editors at PhytoKeys to the Pensoft-PhytoKeys-branded booth at the XX International Botanical Congress in July 2024 (Spain).

In 2024, we presented our journals and publishing opportunities at about 20 scientific forums, including the XX International Botanical Congress (July, Spain), the 12th International Mycological Congress (August, the Netherlands), the 10th World Congress of Herpetology (August, Malaysia) and the XXVII International Congress of Entomology (August, Japan).

Pensoft as a scientific technology provider

We cannot possibly comment on Pensoft’s tech progress in 2024 without mentioning the EU-funded project BiCIKL (acronym for Biodiversity Community Integrated Knowledge Library) that we coordinated for three years ending up last April. 

This 36-month endeavour saw 14 member institutions and 15 research infrastructures representing diverse actors from the biodiversity data realm come together to improve bi-directional links between different platforms, standards, formats and scientific fields. 

Following these three years of collaborative work, we reported a great many notable research outputs from our consortium (find about them in the open-science project collection in the Research Ideas and Outcomes journal, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective”) that culminated in the Biodiversity Knowledge Hub: a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks; and also a set of policy recommendations addressing key policy makers, research institutions and funders who deal with various types of data about the world’s biodiversity, and are thereby responsible to ensuring there findability, accessibility, interoperability and reusability (FAIR-ness).

The Biodiversity Knowledge Hub
Visit the Biodiversity Knowledge Hub: the main product of the BiCIKL consortium at: https://biodiversityknowledgehub.eu/.

Apart from coordinating BiCIKL, we also worked side-by-side with our partners to develop, refine and test each other’s tools and services, in order to make sure that they communicate efficiently with each other, thereby aligning with the principles of FAIR data and the needs of the scientific community in the long run.

During those three years we made a lot of refinements to our OpenBiodiv: a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System, and our ARPHA Writing Tool. The latter is an XML-based online authoring environment using a large set of pre-formatted templates, where manuscripts are collaboratively written, edited and submitted to participating journals published on ARPHA Platform. What makes the tool particularly special is its multiple features that streamline and FAIRify data publishing as part of a scientific publication, especially in the field of biodiversity knowledge. In fact, we made enough improvements to the ARPHA Writing Tool that we will be soon officially releasing its 2.0 version!

OpenBiodiv – The Open Biodiversity Knowledge Management System
ARPHA Writing Tool 2.0

Amongst our collaborative projects are the Nanopublications for Biodiversity workflow that we co-developed with KnowledgePixels to allow researchers to ‘fragment’ their most important scientific findings into machine-actionable and machine-interpretable statements. Being the smallest units of publishable information, these ‘pixels of knowledge’ present an assertion about anything that can be uniquely identified and attributed to its author and serve to communicate a single statement, its original source (provenance) and citation record (publication info).

Nanopublications for Biodiversity

In partnership with the Swiss-based Text Mining group of Patrick Ruch at SIB and the text- and data-mining association Plazi, we brought the SIB Literature Services (SIBiLS) database one step closer to solidifying its “Biodiversity PMC” portal and working title.

Towards the “Biodiversity PMC”: a literature database supporting advanced content queries

Understandably, we spent a lot of effort, time and enthusiasm in raising awareness about our most recent innovations, in addition to our long-standing workflows, formats and tools developed with the aim to facilitate open and efficient access to scientific data; and their integration into published scholarly work, as well as receiving well-deserved recognition for their collection.

We just can’t stress it enough how important and beneficial it is for everyone to have high-quality FAIR data, ideally made available within a formal scientific publication!    

Pensoft’s CTO Teodor Georgiev talks about innovative methods and good practices in the publication of biodiversity data in scholarly papers at the First national meeting of the Bulgarian Barcode of Life (BgBOL) consortium (December, Bulgaria).
Pensoft’s CEO and founder Prof. Dr. Lyubomir Penev presenting his “Data papers on biodiversity” talk at the “Biodiversity data in montane and arid Eurasia” symposium jointly organized by GBIF and by the Institute of Zoology of Republic of Kazakhstan (November, Kazakhstan).

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Pensoft’s CTO Teodor Georgiev presents new features and workflows currently in testing at the ARPHA Writing Tool 2.0 at the EASE Autumn Symposium 2024 (online event).

Pensoft’s Head of Journal development, Marketing and PR Iva Boyadzhieva talks about Pensoft’s data publishing approach and innovations at the German Ecological Society 53rd Annual Conference (September, Germany).

Pensoft as a science communicator

At our Project team, which is undoubtedly the fastest developing department at Pensoft, science communicators are working closely with technology and publishing teams to help consortia bring their scientific results closer to policy actors, decision-makers and the society at large.

Ultimately, bridging the notorious chasm between researchers and global politics boils down to mutual understanding and dialogue. 

Pensoft’s communication team attended COP16 (November 2024, Colombia) along with partners at the consortia of CO-OP4CBD, BioAgora and RESPIN: three Horizon Europe projects, whose communication and dissemination is led by Pensoft.

Throughout 2024, the team, comprising 20 science communicators and project managers, has been working as part of 27 EU-funded project consortia, including nine that have only started this year (check out all partnering projects on the Pensoft website, ordered from most recently started to oldest). Apart from communicating key outcomes and activities during the duration of the projects, at many of the projects, our team has also been actively involved in their grant proposal drafting, coordination, administration, platform development, graphic and web design and others (see all project services offered by Pensoft to consortia).

Naturally, we had a seat on the front row during many milestones achieved by our partners at all those 27 ongoing projects, and communicated to the public by our communicators. 

Amongst those are the release of the InsectsCount web application developed within the Horizon 2020 project SHOWCASE. Through innovative gamification elements, the app encourages users to share valuable data about flower-visiting insects, which in turn help researchers gain new knowledge about the relationship between observed species and the region’s land use and management practices (learn more about InsectsCount on the SHOWCASE prroject website). 

Another fantastic project output was the long-awaited dataset of maps of annual forest disturbances across 38 European countries derived from the Landsat satellite data archive published by the Horizon Europe project ForestPaths in April (find more about the European Forest Disturbance Atlas on the ForestPaths project website).

In a major company highlight, last month, our project team participated in COP29 in Baku, Azerbaijan with a side event dedicated to the role of open science and science communication in climate- and biodiversity-friendly policy.

Pensoft’s participation at COP29 – as well as our perspective on FAIR data and open science – were recently covered in an interview by Exposed by CMD (a US-based news media accredited to cover the event) with our science communicator Alexandra Korcheva and project manager Boris Barov. 

You see, A LOT of great things worth celebrating happened during the year for us at Pensoft: all thanks to ceaselessly flourishing collaboration based on transparency, trust and integrity. Huge ‘THANK YOU!’ goes to everyone who has joined us in our endeavours!

Here’s to many more shared achievements coming up in 2025!

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Now, to keep up with our next steps in real time, we invite you to follow Pensoft on social media on BlueSky, X, Facebook, Instagram and Linkedin! 

Don’t forget to also enter your email to the right to sign up for new content from this blog!

The International Biogeography Society relaunches flagship journal Frontiers of Biogeography on ARPHA platform

“This switch of our journal to a cutting-edge platform, and its committed team of editors, should continue to raise the journal’s visibility and impact,” comments Prof. Dr. Susanne Renner, TIBS President.

The International Biogeography Society (TIBS) has relaunched its flagship open-access scientific journal, Frontiers of Biogeography (FoB), on the ARPHA platform, where it will be co-published with Pensoft Publishers.

This collaboration underscores the society’s commitment to maintaining high-quality, high-visibility and low-cost open-access publishing for the biogeographical community.

“This switch of our journal to a cutting-edge platform, and its committed team of editors, should continue to raise the journal’s visibility and impact,”

comments Prof. Dr. Susanne Renner, TIBS President.

Established by TIBS in 2009, Frontiers of Biogeography serves as an independent forum for research dissemination, and publishes studies on all geographical variations of life at all levels of organisation. The journal adheres to rigorous academic standards, reflecting the mission of TIBS to promote and advance public understanding of biogeographical sciences. 

The journal’s editorial leadership includes Prof. Robert J. Whittaker (University of Oxford, United Kingdom), Dr. Janet Franklin (San Diego State University, USA) and Prof. Mark J. Costello (Nord University, Norway), all esteemed figures in the field.

Frontiers of Biogeography was launched on the ARPHA Platform on the 1st of July 2024. The platform is now open for new submissions and offers a robust review and publication process. Articles and supplementary materials published on ARPHA will be distributed under the Creative Commons Attribution Licence (CC BY 4.0), ensuring wide accessibility and reuse. All previously published issues on the e-Scholarship platform will remain freely accessible, ensuring the continuity of knowledge dissemination.

Frontiers of Biogeography has recently been selected for inclusion in the Web of Science™. Beginning with volume 14(1), articles will be indexed in Emerging Sources Citation Index, Zoological Record, Biological Abstracts, and BIOSIS Previews, significantly enhancing the journal’s visibility.

Furthermore, the journal’s latest Scopus CiteScore of 4.3 places it in the Q1 category for Ecology and Ecology, Evolution, Behaviour and Systematics, and elevates it from Q3 to Q2 in the Global and Planetary Change category.

“I am looking forward to working with the new platform and to the start of a new partnership with our colleagues at Pensoft Publishers. This arrangement underlines the commitment of The International Biogeography Society to the growth and success of Frontiers of Biogeography as a service to our members and the broader scientific community,”

stated Prof. Dr. Robert J. Whittaker, Editor-in-Chief.

“In these days of sometimes exorbitant costs to pay publication charges by some of the big publishers, TIBS and Pensoft are joining forces to make it possible for all authors to be able to publish their work at reasonable costs while maintaining the high scholarly standards of peer-review and editorial management which are the foundation of good science,”

added Prof. Dr. Mark J. Costello, Co-Editor-in-Chief.

“We are excited to welcome Frontiers of Biogeography to the ARPHA Platform and look forward to a successful, open-access future. This partnership aligns with our mission to support scientific research through innovative publishing solutions,”

said Prof. Dr. Lyubomir Penev, CEO and founder of Pensoft Publishers.

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Visit the Frontiers of Biogeography’s new website at https://biogeography.pensoft.net/. Use the Email alert field on the homepage to follow the latest publications, news, and highlights from Frontiers of Biogeography.

You can also follow the journal on X (formerly Twitter) at @newbiogeo.

Keep up to date with the latest from TIBS by following them on X (@Biogeography) and joining the society’s Facebook group.

Brand new computer language describes organismal traits to create computable species descriptions

Describing traits with Phenoscript is like programming a computer code for how an organism looks.

The beetle species Grebennikovius basilewskyi. Numbers next to arrows indicate patterns of phenotype statements explained in the section “Phenoscript: main patterns of phenotype statements”. Arrow numbers from T1 to T5 illustrate individual body parts. See more in the research study.

One of the most beautiful aspects of Nature is the endless variety of shapes, colours and behaviours exhibited by organisms. These traits help organisms survive and find mates, like how a male peacock’s colourful tail attracts females or his wings allow him to fly away from danger. Understanding traits is crucial for biologists, who study them to learn how organisms evolve and adapt to different environments.

To do this, scientists first need to describe these traits in words, like saying a peacock’s tail is “vibrant, iridescent, and ornate”. This approach works for small studies, but when looking at hundreds or even millions of different animals or plants, it’s impossible for the human brain to keep track of everything.

Computers could help, but not even the latest AI technology is able to grasp human language to the extent needed by biologists. This hampers research significantly because, although scientists can handle large volumes of DNA data, linking this information to physical traits is still very difficult.

To solve this problem, researchers from the Finnish Museum of Natural History, Giulio Montanaro and Sergei Tarasov, along with collaborators, have created a special language called Phenoscript. This language is designed to describe traits in a way that both humans and computers can understand. Describing traits with Phenoscript is like programming a computer code for how an organism looks.

Phenoscript uses something called semantic technology, which helps computers understand the meaning behind words, much like how modern search engines know the difference between the fruit “apple” and the tech company “Apple” based on the context of your search.

“This language is still being tested, but it shows a lot of promise. As more scientists start using Phenoscript, it will revolutionise biology by making vast amounts of trait data available for large-scale studies, boosting the emerging field of phenomics,”

explains Montanaro.

In their research article, newly published in the open-access, peer-reviewed Biodiversity Data Journal, the researchers make use of the new language for the first time, as they create semantic phenotypes for four species of dung beetles from the genus Grebennikovius. Then, to demonstrate the power of the semantic approach, they apply simple semantic queries to the generated phenotypic descriptions. 

Finally, the team takes a look yet further ahead into modernising the way scientists work with species information. Their next aim is to integrate semantic species descriptions with the concept of nanopublications, “which encapsulates discrete pieces of information into a comprehensive knowledge graph”. As a result, data that has become part of this graph can be queried directly, thereby ensuring that it remains Findable, Accessible, Interoperable and Reusable (FAIR) through a variety of semantic resources.

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Research paper:

Montanaro G, Balhoff JP, Girón JC, Söderholm M, Tarasov S (2024) Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae). Biodiversity Data Journal 12: e121562. https://doi.org/10.3897/BDJ.12.e121562

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The hereby study is the latest addition to the special topical collection: “Linking FAIR biodiversity data through publications: The BiCIKL approach”, launched and supported by the recently concluded Horizon 2020 project: Biodiversity Community Integrated Knowledge Library (BiCIKL). The collection aims to bring together scientific publications that demonstrate the advantages and novel approaches in accessing and (re-)using linked biodiversity data.

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What expert recommendations did the BiCIKL consortium give to policy makers and research funders to ensure that biodiversity data is FAIR, linked, open and, indeed, future-proof? Find out in the blog post summarising key lessons learnt from the Horizon 2020 project.

How to ensure biodiversity data are FAIR, linked, open and future-proof?

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Follow Biodiversity Data Journal on Facebook and X.

Brand new journal Estuarine Management and Technologies streamlines innovation in ecosystems conservation

There has been an increasing need to support the exchange of research related to the conservation and sustainable management of estuarine ecosystems by means of new-age technologies and approaches.

Where freshwater rivers meet seas and oceans lies a scientifically intriguing and ecologically important type of ecosystem. As estuarine ecosystems provide various and diverse services to humanity and the planet at large, including food security and natural buffers and filters in the events of storms and water pollution, there has been an increasing need to facilitate and support the exchange of research findings and ideas related to their conservation and sustainable management by means of new-age technology and novel approaches.

This is how a team of renowned and passionate scientists, headed by Dr. Soufiane Haddout (Ibn Tofail University, Morocco), took the decision to launch a brand new open-access, peer-reviewed scholarly, aptly titled Estuarine Management and Technologies. They explain the rationale behind the journal in a new editorial, published to mark the official launch of the journal.

Having already worked closely with the scientific publisher and technology provider Pensoft on the fine touches of the concept of the new academic title, the team opted to use Pensoft’s publishing platform of ARPHA. As a result, the new journal provides a seamless, end-to-end publishing experience, encompassing all stages between manuscript submission and article publication, indexation, dissemination and permanent archiving. 

Within the collaboration between the journal’s and Pensoft’s teams, Estuarine Management and Technologies will take advantage of various services offered by the ARPHA platform, including full-text automated export in machine-readable and minable JATS-XML format to over 60 relevant databases for scientific literature and data; semantically enriched and multimedia-friendly publications accessible in HTML; and rich statistics about the outreach and usage of each published article and its elements (e.g. figures and tables), including views, downloads, online mentions, and citations. 

The publishing platform’s in-house indexing team will continue their close work with the journal’s editors to ensure that the scholarly outlet retains highest quality and integrity, so that it covers the criteria for indexation at additional key databases that require individual evaluation. In the meantime, ARPHA’s technical and editorial teams will provide technical and customer support to authors, editors and reviewers. The marketing and promotion team of ARPHA will be also joining forces with the journal to boost the visibility and image of the new academic title.

During the launch phase, content accepted for publication following double-blinded peer review will be made public right away for free to both authors and readers, where the journal will be operating under a continuous publication model.

Estuarine Management and Technologies welcomes studies from a wide spectrum of disciplines, including physics, chemistry, geology, biology, and hydrology, with a focus on interdisciplinarity, multifaceted approaches and holistic perspectives.

“One crucial aspect of estuarine management is the sustainable use of resources to balance conservation with human needs. Striking this delicate equilibrium requires a holistic understanding of the intricate web of ecological interactions within estuarine environments. Advanced technologies, such as isotopic techniques, environmental DNA (eDNA) analysis, can provide insights into the biodiversity of estuarine ecosystems with unprecedented precision,”

explain Dr Haddout and his colleagues in the opening editorial.

Amongst the unique features of the new journal are several additional publication types, such as Expert View, Video Paper, Rapid Communication, Mini Review and Estuarine Scientists, where these have been added to traditional publication outputs (e.g. Research Paper, Review Paper, Data Paper) to foster collaboration between researchers and other stakeholders in the field.

The journal is also running an annual Trailblazing Talent in Estuarine Management and Technologies award intended to recognise and encourage young scientists and engineers at the forefront of cutting-edge research in estuarine management and technologies. Nominations and applications are currently open.

Estuarine Management and Technologies also welcomes applications for guest editors in order to further expand the journal and its immediate expert network.

“I am delighted to see the Estuarine Management and Technologies journal already live on the ARPHA platform. We are confident that this particularly important, yet so far quite overlooked area of study will greatly benefit from this highly promising journal,”

says Prof. Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

“I am pleased to announce the launch of the Estuarine Management and Technologies journal on ARPHA, a decision rooted in our commitment to advancing the field. We believe that this strategic partnership will not only enhance the visibility and accessibility of our journal, but will also foster collaboration and innovation within the estuarine management and technologies community. We expect this alliance to be a catalyst for scholarly excellence, providing a robust platform for researchers and practitioners to share insights, address challenges, and propel the field forward. Together with ARPHA, we are confident in the positive impact our journal will have on shaping the future of estuarine management and technologies.”

says Dr. Soufiane Haddout, Editor-in-Chief and founder, Estuarine Management and Technologies.

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You can visit the journal website and sign up for its newsletter from the homepage.

You can also follow Estuarine Management and Technologies on X (formerly Twitter).

BiCIKL Project supports article collection in Biodiversity Data Journal about use of linked data

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 at least two of the conditions listed below. In the submission form, the author needs to specify the condition(s) applicable to the manuscript. The author should provide the explanation in a cover letter, using the Notes to the editor field.

All submissions must abide by the community-agreed standards for terms, ontologies and vocabularies used in biodiversity informatics. 

The data used in the articles must comply with the Data Quality Checklist and Fair Data Checklist available in the Authors’ instructions of the journal.

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?

All manuscripts submitted to the Biodiversity Data Journal have their data audited by data scientists prior to the peer review stage.

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.

Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

The OpenBiodiv contribution to BiCIKL

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.

Sample of predefined SPARQL queries at OpenBiodiv.

“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,”

concludes Prof Lyubomir Penev.

***

Follow BiCIKL on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

You can also follow Pensoft on Twitter, Facebook and Linkedin and use #OpenBiodiv on Twitter.

Volunteer “community scientists” do a pretty darn good job generating usable data

When museum-goers did a community science activity in an exhibit at the Field Museum (USA), the data they produced were largely accurate.

Left: Cuong Pham, Jimmy Crigler, and Joshua Torres working on a community science platform in an exhibit at the Field Museum (photo by Melanie Pivarski, Roosevelt University).
Right: The microscopic leaves of a liverwort, a primitive plant that helps scientists track climate change (photo by Lauren Johnson, Field Museum).
Original publication by the Field Museum

Ask any scientist — for every “Eureka!” moment, there’s a lot of less-than-glamorous work behind the scenes. Making discoveries about everything from a new species of dinosaur to insights about climate change entails some slogging through seemingly endless data and measurements that can be mind-numbing in large doses.

Community science shares the burden with volunteers who help out, for even just a few minutes, on collecting data and putting it into a format that scientists can use. But the question remains how useful these data actually are for scientists. 

A new study, authored by a combination of high school students, undergrads and grad students, and professional scientists showed that when museum-goers did a community science activity in an exhibit, the data they produced were largely accurate, supporting the argument that community science is a viable way to tackle big research projects.

“It was surprising how all age groups from young children, families, youth, and adults were able to generate high-quality taxonomic data sets, making observations and preparing measurements, and at the same time empowering community scientists through authentic contributions to science,”

says Matt von Konrat (Field Museum, USA), an author of the paper in the journal Research Ideas and Outcomes (RIO Journal) and the head of plant collections at Chicago’s Field Museum.

“This study demonstrates the wonderful scientific outcomes that occur when an entire community comes together,”

says Melanie Pivarski, an associate professor of mathematics at Roosevelt University (USA) and the study’s lead author.

“We were able to combine a small piece of the Field Museum’s vast collections, their scientific knowledge and exhibit creation expertise, the observational skills of biology interns at Northeastern Illinois University (USA), led by our collaborator Tom Campbell, and our Roosevelt University student’s data science expertise. The creation of this set of high-quality data was a true community effort!” 

The study focuses on an activity in an exhibition at the Field Museum, in which visitors could partake in a community science project. In the community science activity, museumgoers used a large digital touchscreen to measure the microscopic leaves photographs of plants called liverworts. 

These tiny plants, the size of an eyelash, are sensitive to climate change, and they can act like a canary in a coal mine to let scientists know about how climate change is affecting a region. It’s helpful for scientists to know what kinds of liverworts are present in an area, but since the plants are so tiny, it’s hard to tell them apart. The sizes of their leaves (or rather, lobes — these are some of the most ancient land plants on Earth, and they evolved before true leaves had formed) can hint at their species. But it would take ages for any one scientist to measure all the leaves of the specimens in the Field’s collection. Enter the community scientists.

“Drawing a fine line to measure the lobe of a liverwort for a few hours can be mentally strenuous, so it’s great to have community scientists take a few minutes out of their day using fresh eyes to help measure a plant leaf. A few community scientists who’ve helped with classifying acknowledged how exciting it is knowing they are playing a helping hand in scientific discovery,”  

says Heaven Wade, a research assistant at the Field Museum who began working on the MicroPlants project as an undergraduate intern.

Community scientists using the digital platform measured thousands of microscopic liverwort leaves over the course of two years.

“At the beginning, we needed to find a way to sort the high quality measurements out from the rest. We didn’t know if there would be kids drawing pictures on the touchscreen instead of measuring leaves or if they’d be able to follow the tutorial as well as the adults did. We also needed to be able to automate a method to determine the accuracy of these higher quality measurements,”

says Pivarski.

To answer these questions, Pivarski worked with her students at Roosevelt University to analyze the data. They compared measurements taken by the community scientists with measurements done by experts on a couple “test” lobes; based on that proof of concept, they went on to analyze the thousands of other leaf measurements. The results were surprising.

“We were amazed at how wonderfully children did at this task; it was counter to our initial expectations. The majority of measurements were high quality. This allowed my students to create an automated process that produced an accurate set of MicroPlant measurements from the larger dataset,”

says Pivarski.

The researchers say that the study supports the argument that community science is valuable not just as a teaching tool to get people interested in science, but as a valid means of data collection.

“Biological collections are uniquely poised to inform the stewardship of life on Earth in a time of cataclysmic biodiversity loss, yet efforts to fully leverage collections are impeded by a lack of trained taxonomists. Crowd-sourced data collection projects like these have the potential to greatly accelerate biodiversity discovery and documentation from digital images of scientific specimens,”

says von Konrat.
Research article:

Pivarski M, von Konrat M, Campbell T, Qazi-Lampert AT, Trouille L, Wade H, Davis A, Aburahmeh S, Aguilar J, Alb C, Alferes K, Barker E, Bitikofer K, Boulware KJ, Bruton C, Cao S, Corona Jr. A, Christian C, Demiri K, Evans D, Evans NM, Flavin C, Gillis J, Gogol V, Heublein E, Huang E, Hutchinson J, Jackson C, Jackson OR, Johnson L, Kirihara M, Kivarkis H, Kowalczyk A, Labontu A, Levi B, Lyu I, Martin-Eberhardt S, Mata G, Martinec JL, McDonald B, Mira M, Nguyen M, Nguyen P, Nolimal S, Reese V, Ritchie W, Rodriguez J, Rodriguez Y, Shuler J, Silvestre J, Simpson G, Somarriba G, Ssozi R, Suwa T, Syring C, Thirthamattur N, Thompson K, Vaughn C, Viramontes MR, Wong CS, Wszolek L (2022) People-Powered Research and Experiential Learning: Unravelling Hidden Biodiversity. Research Ideas and Outcomes 8: e83853. https://doi.org/10.3897/rio.8.e83853

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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.

***

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.

48 years of Australian collecting trips in one data package

From 1973 to 2020, Australian zoologist Dr Robert Mesibov kept careful records of the “where” and “when” of his plant and invertebrate collecting trips. Now, he has made those valuable biodiversity data freely and easily accessible via the Zenodo open-data repository, so that future researchers can rely on this “authority file” when using museum specimens collected from those events in their own studies. The new dataset is described in the open-access, peer-reviewed Biodiversity Data Journal.

While checking museum records, Dr Robert Mesibov found there were occasional errors in the dates and places for specimens he had collected many years before. He was not surprised.

“It’s easy to make mistakes when entering data on a computer from paper specimen labels”, said Mesibov. “I also found specimen records that said I was the collector, but I know I wasn’t!”

One solution to this problem was what librarians and others have long called an “authority file”.

“It’s an authoritative reference, in this case with the correct details of where I collected and when”, he explained.

“I kept records of almost all my collecting trips from 1973 until I retired from field work in 2020. The earliest records were on paper, but I began storing the key details in digital form in the 1990s.”

The 48-year record has now been made publicly available via the Zenodo open-data repository after conversion to the Darwin Core data format, which is widely used for sharing biodiversity information. With this “authority file”, described in detail in the open-access, peer-reviewed Biodiversity Data Journal, future researchers will be able to rely on sound, interoperable and easy to access data, when using those museum specimens in their own studies, instead of repeating and further spreading unintentional errors.

“There are 3829 collecting events in the authority file”, said Mesibov, “from six Australian states and territories. For each collecting event there are geospatial and date details, plus notes on the collection.”

Mesibov hopes the authority file will be used by museums to correct errors in their catalogues.

“It should also save museums a fair bit of work in future”, he explained. “No need to transcribe details on specimen labels into digital form in a database, because the details are already in digital form in the authority file.”

Mesibov points out that in the 19th and 20th centuries, lists of collecting events were often included in the reports of major scientific expeditions.

“Those lists were authority files, but in the pre-digital days it was probably just as easy to copy collection data from specimen labels.”

“In the 21st century there’s a big push to digitise museum specimen collections”, he said. “Museum databases often have lookup tables with scientific names and the names of collectors. These lookup tables save data entry time and help to avoid errors in digitising.”

“Authority files for collecting events are the next logical step,” said Mesibov. “They can be used as lookup tables for all the important details of individual collections: where, when, by whom and how.”

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Research paper:

Mesibov RE (2021) An Australian collector’s authority file, 1973–2020. Biodiversity Data Journal 9: e70463. https://doi.org/10.3897/BDJ.9.e70463

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Robert Mesibov’s webpage: https://www.datafix.com.au/mesibov.html

Robert Mesibov’s ORCID page: https://orcid.org/0000-0003-3466-5038