Tag: scientific

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.”

###

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

###

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

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

🎉Celebration time: here’s to 1,000 issues of ZooKeys!

With the 1,000th ZooKeys issue now hot off the press, the time has come to celebrate the millennium of Pensoft’s very first scientific journal: ZooKeys!

With the 1,000th ZooKeys issue now hot off the press, the time has come to celebrate the millennium of Pensoft’s very first scientific journal: ZooKeys!

In fact, the cause for celebration is two-fold: this year, it’s also the 10th anniversary of ZooKeys’ very special 50th issue, which marked a new era for biodiversity data publishing by introducing several innovative workflows and tools. This is when ZooKeys became an example to follow globally: a title the journal still takes pride to be holding to this day.

Articles published in ZooKeys since the journal’s launch in 2008 (data from 3/12/2020).

Today, we shall reminisce about everything along the way: from that sunny Californian morning at the Entomological Society of America meeting in 2007, where the idea about a new-age taxonomic journal in zoology sprang up in a breakfast chat between renowned entomologists and future founders of ZooKeys: Prof Lyubomir Penev and Dr Terry Erwin, to this very moment, where we’re counting over 5,500 published articles, authored by more than 8,000 researchers from 144 countries and comprising ~150,000 pages. Thus, we saw the description of one supertribe, seven tribes, five subtribes, 27 families, over 800 genera and more than 12,000 species previously unknown to science. In this journey, ZooKeys climbed up the ladder of academic rigour and trustability to become today’s most prolific open-access journal of zoology.

Even though today is the time to feel exalted and look back on our achievements and conquered milestones with ear-to-ear smiles, it is with heavy hearts that we’ll be raising our glasses tonight, as we won’t be joined by our beloved friend and founding Editor-in-Chief, Dr Terry Erwin, whom we lost on 11th May 2020. While his place in our hearts and ZooKeys’ Editorial board will never be filled, we accept our duty to help for his legacy to persist for the future generations of scientists by taking a vow to never lower our standards or cease to improve our services and care for our readers, authors, reviewers and editors alike. 

In honour of Terry, who will be remembered for his splendid personality and zealous enthusiasm for carabid beetles and the world’s immense biodiversity, we’ve opened up a special memorial volume to be published on 11th May 2021.

In fact, we have thousands of people to thank for the place ZooKeys is at right now: these are our authors, who have trusted us with their research work time and time again; our reviewers and editors, who have taken their invaluable time to promptly process submitted manuscripts; and, of course, our readers, who are using ZooKeys content to expand the world’s knowledge, either by learning and building on the findings in their own research, or by spreading the knowledge to those who will.

With a thought for our authors & readers

We’ve been striving to implement the latest and most convenient scholarly publishing technologies and innovations, and also develop some of our own to make sure that ZooKeys users enjoy their experience with our flagship journal. 

In hindsight, ZooKeys was the first journal to pioneer a lot of scholarly publishing technologies, which back in the time were quite revolutionary. Notable examples from 2008-2016 include: 

Yet, this was only the beginning. Fast forward to December 2020, we’re working even harder to build up on our achievements and evolve, so that we stay on top of our game and the scholarly publishing scene. Here are the key innovations we recently implemented in ZooKeys:

With a thought for our editors

Besides revolutionising research publishing, at Pensoft, we’re also deeply devoted to facilitating our editors in their day-to-day editorial work, as well as their long-term engagement with the journal and its progress. 

Recently, we expanded journal performance reporting services, in order to keep our editors on track with the most recent trends in their journal’s performance. Meanwhile, we’ve also taken care after the continuous improvement in those stats by implementing several features meant to facilitate and expedite the handling of manuscripts.

New features in ARPHA to aid journal editors in day-to-day activities and long-term strategic decisions
Follow ARPHA’s blog to keep up with the new features available to users of Pensoft’s journals and all journals hosted on ARPHA Platform.  

With a thought for the community

Naturally, research outputs are only as valuable to publish as they are valuable to the community: within and beyond academia. Ultimately, their merit is best measured by citations and readership. This is why, we shall now have a look back at the most impactful papers published in ZooKeys to date.

Author’s delight

Thanks to the indexation of ZooKeys in the research citation database of Dimensions, following the collaboration between ARPHA and Digital Science, which started in 2018, we’re now able to explore the all-time most cited publications in our flagship journal. Detailed information and links to the papers where each of those studies has been cited is available on the webpage of the article.

  1. Supporting Red List threat assessments with GeoCAT: geospatial conservation assessment tool (DOI: 10.3897/zookeys.150.2109)
  2. Family-group names in Coleoptera (Insecta) (DOI: 10.3897/zookeys.88.807)
  3. Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication (DOI: 10.3897/zookeys.219.3944)  
  4. Forty years of carabid beetle research in Europe – from taxonomy, biology, ecology and population studies to bioindication, habitat assessment and conservation (DOI: 10.3897/zookeys.100.1523) 
  5. Useful model organisms, indicators, or both? Ground beetles (Coleoptera, Carabidae) reflecting environmental conditions (DOI: 10.3897/zookeys.100.1533) 

Reader’s delight

Thanks to ARPHA Platform’s all-roundedness and transparency, we get to explore the most read papers ever published in ZooKeys straight from the Articles section on the journal’s website.

  1. Taxonomic revision of the olingos (Bassaricyon), with description of a new species, the Olinguito (DOI: 10.3897/zookeys.324.5827)

In 2013, ZooKeys had the honour to announce the first carnivore found in the Western Hemisphere in over three decades. Further, that wasn’t ANY carnivore, but the olinguito, which National Geographic rightfully called a “fuzzy fog-dweller with a face like a teddy bear”.

  1. An extraordinary new family of spiders from caves in the Pacific Northwest (Araneae, Trogloraptoridae) (DOI: 10.3897/zookeys.215.3547)

A year prior to the description of the olinguito, a brand new family of “cave robbing” spiders emerged from the pages of ZooKeys, after US scientists found a previously unknown to science spider with “unique, toothed claws at the end of each leg” in Oregon.

  1. Family-Group Names In Coleoptera (Insecta) (DOI: 10.3897/zookeys.88.807)

A huge, first-of-its-kind catalogue containing data on all family-group names for all known extant and fossil beetles (order Coleoptera) was published in ZooKeys in an exemplary research collaboration, spanning three continents in 2011.

  1. Review of Neopalpa Povolný, 1998 with description of a new species from California and Baja California, Mexico (Lepidoptera, Gelechiidae) (DOI: 10.3897/zookeys.646.11411)

In a truly world-wide sensation, a new species of tiny moth inhabiting a narrow stretch of extremely fragile habitat running between the USA and Mexico, was named after then President-elect Donald Trump in a desperate call to protect this and other similarly vulnerable ecosystems in North America. The species currently goes by the name Neopalpa donaldtrumpi.

  1. Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States (DOI: 10.3897/zookeys.560.6264)

In 2016, US scientists described a total of 14 new to science tarantula species from what many would think to be one the best-researched countries: the United States of America. Curiously enough, one of those tarantula species, found in California near Folsom Prison – a place best known from Cash’s song “Folsom Prison Blues”, was aptly named Aphonopelma johnnycashi.  

Public’s delight

As visionaries, we’ve long realised that scientific impact goes beyond citations and journal subscribers. Communicating science to the community beyond academia is, in fact, one of the strongest components in research dissemination, as it lets the laypeople make sense of the wider world and where exactly they stand in the bigger picture. This is why we’ve been putting that special extra effort to promote research published in our journals–including ZooKeys–using press releases, blog posts and social media content (follow ZooKeys on Twitter and Facebook).

Data source: Altmetric.

Thanks to our partnership with Altmetric, we’re able to identify the top five most popular papers from ZooKeys for all times. These are the ones that have sparkled the most online discussions via social media, big news headlines, blog posts, Wikipedia and more.

  1. Review of Neopalpa Povolný, 1998 with description of a new species from California and Baja California, Mexico (Lepidoptera, Gelechiidae) (DOI: 10.3897/zookeys.646.11411)

Not only was the previously undescribed species of moth subject to a serious threat of extinction, having been exclusively known from a fragmented area along the Mexico–United States border, but the insect’s “hairstyle” was pointed out to bear a striking resemblance to the golden locks of the 45th U.S. President Donald Trump.

Credit: CNN (read the full news story here)
  1. Geology and paleontology of the Upper Cretaceous Kem Kem Group of eastern Morocco (DOI: 10.3897/zookeys.928.47517)

Published in ZooKeys earlier this year, this extensive geology and paleontology monograph presents an unprecedented in its volume and scientific value account of a large portion of the most important prehistoric vertebrate fossils ever unearthed from the famous Kem Kem beds in Morocco. “A monograph larger than Paralititan,” as a Reddit user justly pointed out.

A monograph larger than Paralititan about Kem Kem Beds: Stratigraphy, vertebrate zoology, palaeoecosystem, and a lot more. If you ever wanted a primary source to research that Formation, this is your place. from Dinosaurs
  1. Taxonomic revision of the tarantula genus Aphonopelma Pocock, 1901 (Araneae, Mygalomorphae, Theraphosidae) within the United States (DOI: 10.3897/zookeys.560.6264)

On top of taking pride in becoming the discoverer of as many as 14 tarantula species living “right under our noses” in the US, Dr Chris Hamilton enjoyed the spotlight of Live television in his appearance on Sky News. So did a lucky specimen of the newly described species: Aphonopelma johnnycashi! Suffice it to say, the tarantula was named after the legendary American singer-songwriter for all the right reasons.

Credit: Sky News (read the full news story here)
  1. Colobopsis explodens sp. n., model species for studies on “exploding ants” (Hymenoptera, Formicidae), with biological notes and first illustrations of males of the Colobopsis cylindrica group (DOI: 10.3897/zookeys.751.22661)

Apparently, ants that rip their bodies apart in a self-sacrificial attempt to save their colonies from enemies, weren’t something new by the time PhD student Alice Laciny and her team described the new to science species Colobopsis explodens from Brunei. However, the study published in ZooKeys in 2018 was the first to conduct and film experiments on the peculiar exploding behaviour. Although not the very first for science, C. explodens was the first “T-ant-T” species to be described since 1935.

  1. Mapping the expansion of coyotes (Canis latrans) across North and Central America (DOI: 10.3897/zookeys.759.15149)

Today, coyotes live all around North America: from Alaska to Panama, California to Maine. Once upon a time, or rather, between the Holocene and the early 1900s, their range used to be restricted to the arid west of North America. So, how did the coyotes turn up at the doorstep of South America? North Carolina scientists reached to natural history collections to map the historic colonisation of the coyotes all the way to our days.

***

In our final remarks on this special occasion, it’s the time to say a special Thank you! to our most prolific authors:

  1. Dr Shuqiang Li, expert on spider taxonomy and systematics at the Chinese Academy of Sciences, who’s also a reviewer and a subject editor at ZooKeys (64 publications).
  2. Dr Michael S. Engel, paleontologist and entomologist at the University of Kansas and the American Museum of Natural History, who is also amongst the top five most active reviewers and the three most active subject editors in ZooKeys (59 publications).
  3. Dr Li-Zhen Li, coleopterist at Shanghai Normal University (57 publications).
  4. Dr Reginald Webster, coleopterist at Natural Resources Canada and a reviewer at ZooKeys (57 publications).
  5. Dr Sergei Golovatch, myriapodologist at the Russian Academy of Sciences, and a reviewer and a subject editor at ZooKeys (53 publications).

As well as to our most active reviewers:

  1. Dr Yuri Marusik, arachnologist at the Russian Academy of Sciences and the University of Free State, Magadan, South Africa. He is also a subject editor at ZooKeys.
  2. Dr Donald Lafontaine, entomologist at the Canadian National Collection of Insects, Arachnids, and Nematodes and Agriculture and Agri-Food Canada. He is also a subject editor at ZooKeys. 
  3. Dr Ivan H. Tuf, ecologist at Palacký University (Czech Republic) and a subject editor at ZooKeys.
  4. Dr Viatcheslav Ivanenko, taxonomist at the Lomonosov Moscow State University.
  5. Dr Michael S. Engel, paleontologist and entomologist at the University of Kansas and the American Museum of Natural History, and also one of the most productive authors and most active subject editors at ZooKeys.

And ZooKeys’ most active editors:

  1. Prof Pavel Stoev, taxonomist, ecologist, and director at the National Natural History Museum (Bulgaria), and managing editor at ZooKeys.
  2. Prof Lyubomir Penev, entomologist, ecologist at the Bulgarian Academy of Sciences and founder of ZooKeys.
  3. Dr Michael S. Engel, paleontologist and entomologist at the University of Kansas and the American Museum of Natural History, and also one of the most productive authors and most active reviewers at ZooKeys.
  4. Dr Nina Bogutskaya, hydrobiologist and ichthyologist at the Museum of Natural History Vienna, and also a reviewer at ZooKeys.
  5. Dr Jeremy Miller, taxonomist and arachnologist at the Naturalis Biodiversity Center (Netherlands), and also a reviewer at ZooKeys.

Looking forward to sharing with you our next milestones and celebrations!

Meanwhile, make sure to follow ZooKeys on Twitter and Facebook to stay in touch!

A decade of ZooKeys: Publishing and communicating knowledge & love for zoology