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.

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A decade of empowering biodiversity science: celebrating 10 years of Biodiversity Data Journal

Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.

Today, 16 September 2023, we are celebrating our tenth anniversary: an important milestone that has prompted us to reflect on the incredible journey that Biodiversity Data Journal (BDJ) has been through.

From the very beginning, our mission was clear: to revolutionise the way biodiversity data is shared, accessed, and harnessed. This journey has been one of innovation, collaboration, and a relentless commitment to making biodiversity data FAIR – Findable, Accessible, Interoperable, and Reusable.

Over the past 10 years, BDJ, under the auspices of our esteemed publisher Pensoft, has emerged as a trailblazing force in biodiversity science. Our open-access platform has empowered researchers from around the world to publish comprehensive papers that seamlessly blend text with morphological descriptions, occurrences, data tables, and more. This holistic approach has enriched the depth of research articles and contributed to the creation of an interconnected web of biodiversity information.

In addition, by utilising ARPHA Writing Tool and ARPHA Platform as our entirely online manuscript authoring and submission interface, we have simplified the integration of structured data and narrative, reinforcing our commitment to simplifying the research process.

One of our most significant achievements is democratising access to biodiversity data. By dismantling access barriers, we have catalysed the emergence of novel research directions, equipping scientists with the tools to combat critical global challenges such as biodiversity loss, habitat degradation, and climate fluctuations.

We firmly believe that data should be openly accessible to all, fostering collaboration and accelerating scientific discovery. By upholding the FAIR principles, we ensure that the datasets accompanying our articles are not only discoverable and accessible, but also easy to integrate and reusable across diverse fields.

As we reflect on the past decade, we are invigorated by the boundless prospects on the horizon. We will continue working on to steer the global research community towards a future where biodiversity data is open, accessible, and harnessed to tackle global challenges.

Ten years of biodiversity research

To celebrate our anniversary, we have curated some of our most interesting and memorable BDJ studies from the past decade.

  • Recently, news outlets were quick to cover a new species of ‘snug’ published in our journal.
  • This Golden Retriever trained to monitor hermit beetle larvae proved once again the incredible capabilities of our canine friends.
Teseo, the Golden Retriever monitoring hermit beetle larvae
  • Who could forget this tiny fly named after the former Governor of California?
  • Or this snail named after climate activist Greta Thunberg?
Craspedotropis gretathunbergae

New discoveries are always exciting, but some of our favourite research focuses on formerly lost species, back where they belong.

  • Like the griffon vulture, successfully reintroduced to Bulgaria after fifty years.

Citizen science has shown time and time again that it holds an important position in biodiversity research.

  • This group, for example, who found a beetle the size of a pinhead in Borneo.
“Life Beneath the Ice”, a short musical film about light and life beneath the Antarctic sea-ice by Dr. Emiliano Cimoli

We extend our heartfelt gratitude to our authors, reviewers, readers, and the entire biodiversity science community for being integral parts of this transformative journey. Together, we have redefined scientific communication, and we will continue to push the boundaries of knowledge.

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Nanopublications tailored to biodiversity data

Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.

First off, why nanopublications?

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability. 

By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data. 

With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable manner in line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.

The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards. 

Now, what’s new?

As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:

  1. Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
  1. Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
  1. Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).

Nanopublications for biodiversity data?

At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proof the most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments

On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.

Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:

So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences. 

Nanopublication template customised for biodiversity research publications available from Nanodash.

As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks. 

The novel domain-specific publication format was launched as part of the collaboration between Knowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisher Pensoft.

… so, what exactly is a nanopublication?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained on nanopub.net.

Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.

These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.

In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs. 

“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”

said Prof. Lyubomir Penev, founder and CEO at Pensoft, which had published the very first semantically enhanced research article in the biodiversity domain back in 2010 in the ZooKeys journal.

Why are nanopublications necessary?

By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragments of scientific information is interconnected and traceable back to its author(s) and scientific evidence. 

A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels. 

By building on shared knowledge representation models, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts. 

Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.

A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way. 

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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal

Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!

This Nanopublications for biodiversity workflow was created with a partial support of the European Union’s Horizon 2020 BiCIKL project under grant agreement No 101007492 and in collaboration with Knowledge Pixels AG.The tool uses data and API services of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, Environmental Ontology (ENVO), Relation Ontology (RO), NOMEN, ZooBank, Index Fungorum, MycoBank, IPNI, TreatmentBank, and other resources. 

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On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.

Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.

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Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.

Call for data papers describing datasets from Northern Eurasia in Biodiversity Data Journal

In collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, GBIF has announced a new call for authors to submit and publish data papers on Russia in a special collection of Biodiversity Data Journal (BDJ). The call extends and expands upon a successful effort in 2020 to mobilize data from European Russia.

GBIF partners with FinBIF and Pensoft’s Biodiversity Data Journal to streamline publication of new datasets about biodiversity from Northern Eurasia

Original post via GBIF

In collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, GBIF has announced a new call for authors to submit and publish data papers on Northern Eurasia in a special collection of Biodiversity Data Journal (BDJ). The call expands upon successful efforts to mobilize data from European Russia in 2020 and from the rest of Russia in 2021.

Until 30 June 2022, Pensoft will waive the article processing fee (normally €650) for the first 50 accepted data paper manuscripts that meet the following criteria for describing a dataset:

See the complete definition of these terms below.

Detailed instructions

Authors must prepare the manuscript in English and submit it in accordance with BDJ’s instructions to authors by 30 June 2022. Late submissions will not be eligible for APC waivers.

Sponsorship is limited to the first 50 accepted submissions meeting these criteria on a first-come, first-served basis. The call for submissions can therefore close prior to the deadline of 30 June 2022. Authors may contribute to more than one manuscript, but artificial division of the logically uniform data and data stories, or “salami publishing”, is not allowed.

BDJ will publish a special issue including the selected papers by the end of 2021. The journal is indexed by Web of Science (Impact Factor 1.225), Scopus (CiteScore: 2.0) and listed in РИНЦ / eLibrary.ru.

For non-native speakers, please ensure that your English is checked either by native speakers or by professional English-language editors prior to submission. You may credit these individuals as a “Contributor” through the AWT interface. Contributors are not listed as co-authors but can help you improve your manuscripts. BDJ will introduce stricter language checks for the 2022 call; poorly written submissions will be rejected prior to the peer-review process.

In addition to the BDJ instruction to authors, data papers must referenced the dataset by
a) citing the dataset’s DOI
b) appearing in the paper’s list of references
c) including “Northern Eurasia 2022” in the Project Data: Title and “N-Eurasia-2022“ in Project Data: Identifier in the dataset’s metadata.

Authors should explore the GBIF.org section on data papers and Strategies and guidelines for scholarly publishing of biodiversity data. Manuscripts and datasets will go through a standard peer-review process. When submitting a manuscript to BDJ, authors are requested to assign their manuscript to the Topical Collection: Biota of Northern Eurasia at step 3 of the submission process. To initiate the manuscript submission, remember to press the Submit to the journal button.

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

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

This project is a continuation of successful calls for data papers from European Russia in 2020 and 2021. The funded papers are available in the Biota of Russia special collection and the datasets are shown on the project page.

Definition of terms

Datasets with more than 7,000 presence records new to GBIF.org

Datasets should contain at a minimum 7,000 presence records new to GBIF.org. While the focus is on additional records for the region, records already published in GBIF may meet the criteria of ‘new’ if they are substantially improved, particularly through the addition of georeferenced locations.” Artificial reduction of records from otherwise uniform datasets to the necessary minimum (“salami publishing”) is discouraged and may result in rejection of the manuscript. New submissions describing updates of datasets, already presented in earlier published data papers will not be sponsored.

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

Datasets with high-quality data and metadata

Authors should start by publishing a dataset comprised of data and metadata that meets GBIF’s stated data quality requirement. This effort will involve work on an installation of the GBIF Integrated Publishing ToolkitBDJ will conduct its standard data audit and technical review. All datasets must pass the data audit prior to a manuscript being forwarded for peer review.

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

Datasets with geographic coverage in Northern Eurasia

In correspondence with the funding priorities of this programme, at least 80% of the records in a dataset should have coordinates that fall within the priority areas of Russia, Ukraine, Belarus, Kazakhstan, Kyrgyzstan, Uzbekistan, Tajikistan, Turkmenistan, Moldova, Georgia, Armenia and Azerbaijan. However, authors of the paper may be affiliated with institutions anywhere in the world.

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Call for data papers describing datasets from Russia to be published in Biodiversity Data Journal

GBIF partners with FinBIF and Pensoft to support publication of new datasets about biodiversity from across Russia

Original post via GBIF

In collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, GBIF has announced a new call for authors to submit and publish data papers on Russia in a special collection of Biodiversity Data Journal (BDJ). The call extends and expands upon a successful effort in 2020 to mobilize data from European Russia.

Between now and 15 September 2021, the article processing fee (normally €550) will be waived for the first 36 papers, provided that the publications are accepted and meet the following criteria that the data paper describes a dataset:

The manuscript must be prepared in English and is submitted in accordance with BDJ’s instructions to authors by 15 September 2021. Late submissions will not be eligible for APC waivers.

Sponsorship is limited to the first 36 accepted submissions meeting these criteria on a first-come, first-served basis. The call for submissions can therefore close prior to the stated deadline of 15 September 2021. Authors may contribute to more than one manuscript, but artificial division of the logically uniform data and data stories, or “salami publishing”, is not allowed.

BDJ will publish a special issue including the selected papers by the end of 2021. The journal is indexed by Web of Science (Impact Factor 1.331), Scopus (CiteScore: 2.1) and listed in РИНЦ / eLibrary.ru.

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

In addition to the BDJ instruction to authors, it is required that datasets referenced from the data paper a) cite the dataset’s DOI, b) appear in the paper’s list of references, and c) has “Russia 2021” in Project Data: Title and “N-Eurasia-Russia2021“ in Project Data: Identifier in the dataset’s metadata.

Authors should explore the GBIF.org section on data papers and Strategies and guidelines for scholarly publishing of biodiversity data. Manuscripts and datasets will go through a standard peer-review process. When submitting a manuscript to BDJ, authors are requested to select the Biota of Russia collection.

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

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

The 2021 extension of the collection of data papers will be edited by Vladimir Blagoderov, Pedro Cardoso, Ivan Chadin, Nina Filippova, Alexander Sennikov, Alexey Seregin, and Dmitry Schigel.

This project is a continuation of the successful call for data papers from European Russia in 2020. The funded papers are available in the Biota of Russia special collection and the datasets are shown on the project page.

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Definition of terms

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

Datasets should contain at a minimum 5,000 new records that are new to GBIF.org. While the focus is on additional records for the region, records already published in GBIF may meet the criteria of ‘new’ if they are substantially improved, particularly through the addition of georeferenced locations.” Artificial reduction of records from otherwise uniform datasets to the necessary minimum (“salami publishing”) is discouraged and may result in rejection of the manuscript. New submissions describing updates of datasets, already presented in earlier published data papers will not be sponsored.

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

Datasets with high-quality data and metadata

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

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

Datasets with geographic coverage in Russia

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

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Check out the Biota of Russia dynamic data paper collection so far.

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New DNA barcoding project aims at tracking down the “dark taxa” of Germany’s insect fauna

New dynamic article collection at Biodiversity Data Journal is already accumulating the project’s findings

About 1.4 million species of animals are currently known, but it is generally accepted that this figure grossly underestimates the actual number of species in existence, which likely ranges between five and thirty million species, or even 100 million. 

Meanwhile, a far less well-known fact is that even in countries with a long history of taxonomic research, such as Germany, which is currently known to be inhabited by about 48,000 animal species, there are thousands of insect species still awaiting discovery. In particular, the orders Diptera (flies) and Hymenoptera (especially the parasitoid wasps) are insect groups suspected to contain a strikingly large number of undescribed species. With almost 10,000 known species each, these two insect orders account for approximately two-thirds of Germany’s insect fauna, underlining the importance of these insects in many ways.

The conclusion that there are not only a few, but so many unknown species in Germany is a result of the earlier German Barcode of Life projects: GBOL I and GBOL II, both supported by the German Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF) and the Bavarian Ministry of Science under the project Barcoding Fauna Bavarica. 

In its previous phases, GBOL aimed to identify all German species reliably, quickly and inexpensively using DNA barcodes. Since the first project was launched twelve years ago, more than 25,000 German animal species have been barcoded. Among them, the comparatively well-known groups, such as butterflies, moths, beetles, grasshoppers, spiders, bees and wasps, showed an almost complete coverage of the species inventory.

In 2020, another BMBF-funded DNA barcoding project, titled GBOL III: Dark Taxa, was launched, in order to focus on the lesser-known groups of Diptera and parasitoid Hymenoptera, which are often referred to as “dark taxa”. The new project commenced at three major German natural history institutions: the Zoological Research Museum Alexander Koenig (Bonn), the Bavarian State Collection of Zoology (SNSB, Munich) and the State Museum of Natural History Stuttgart, in collaboration with the University of Würzburg and the Entomological Society Krefeld. Together, the project partners are to join efforts and skills to address a range of questions related to the taxonomy of the “dark taxa” in Germany.

As part of the initiative, the project partners are invited to submit their results and outcomes in the dedicated GBOL III: Dark Taxa article collection in the peer-reviewed, open-access Biodiversity Data Journal. There, the contributions will be published dynamically, as soon as approved and ready for publication. The articles will include taxonomic revisions, checklists, data papers, contributions to methods and protocols, employed in DNA barcoding studies with a focus on the target taxa of the project.

“The collection of articles published in the Biodiversity Data Journal is an excellent approach to achieving the consortium’s goals and project partners are encouraged to take advantage of the journal’s streamlined publication workflows to publish and disseminate data and results that were generated during the project,”

says the collection’s editor Dr Stefan Schmidt of the Bavarian State Collection of Zoology.

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Find and follow the dynamic article collection GBOL III: Dark Taxa in Biodiversity Data Journal.

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Pensoft partners with ReviewerCredit to certify and reward peer review

Following recent API integration with ReviewerCredits, Pensoft – the scholarly publisher and technology provider – has launched a pilot phase with one of its peer-reviewed, open-access journal: Biodiversity Data Journal (BDJ). Reviewers, who create an account on ReviewerCredits, will automatically record their peer review contributions, which will be certified via the platform and receive rewards and recognition within the scholarly community and fellow scientists.

Following recent API integration with ReviewerCredits, Pensoft – the scholarly publisher and technology provider – has launched a pilot phase with one of its peer-reviewed, open-access journal: Biodiversity Data Journal (BDJ). Reviewers, who create an account on ReviewerCredits, will automatically record their peer review contributions, which will be certified via the platform and receive rewards and recognition within the scholarly community and fellow scientists. 

Apart from a seamless system to showcase their peer review activity, reviewers will also be assigned virtual credits, which can be redeemed for benefits provided by selected partners, including discounted APCs. 

The registration on ReviewerCredits is free. While a reviewer can register any of his/her peer reviews on the platform, reviews for journals partnering with ReviewerCredits earn additional redeemable credits.

Once a reviewer signs in BDJ using their own reviewer account, a pop-up window will recommend that an account on ReviewerCredits is created by using an ORCID ID or an email address. Once the registration is complete, each completed peer review contribution will automatically appear as certified on ReviewerCredits, as soon as the editor submits a final decision on the reviewed manuscript. In line with peer-review confidentiality, the entry displayed on ReviewerCredits will not contain the content of the review, nor the particular paper it is associated with.

“We are happy to partner with ReviewerCredits to further recognise, encourage and reward the contribution of reviewers in BDJ. No one should forget that, at the end of the day, it is up to reviewers to ensure that only good and quality science makes its way in the world. Unfortunately, though, their role in scholarship has traditionally been overlooked and we all need to put in effort to change the status quo,”

comments Prof. Lyubomir Penev, founder and CEO of Pensoft.

“We are excited by the collaboration with Pensoft on this project and to acknowledge BDJ among our prestigious partner journals. Pensoft has proved an extremely competent partner, well aware of the importance for journals to state the value of their peer review process. We work together to strengthen the collaboration between journals and reviewers and we are looking forward to a growing collaboration with Pensoft publications,”

Prof. Giacomo Bellani, co-founder and president of ReviewerCredits, underlines the value and enthusiasm for this new partnership.

About ReviewerCredits:

ReviewerCredits is a startup company, accredited to the University of Milan Bicocca, launched in 2017 by enthusiastic active researchers and scientists. ReviewerCredits is an independent platform dedicated to scientists, Journals and Publishers addressing the peer review process.

Recipe for Reusability: Biodiversity Data Journal integrated with Profeza’s CREDIT Suite

Through their new collaboration, the partners encourage publication of dynamic additional research outcomes to support reusability and reproducibility in science

In a new partnership between open-access Biodiversity Data Journal (BDJ) and workflow software development platform Profeza, authors submitting their research to the scholarly journal will be invited to prepare a Reuse Recipe Document via CREDIT Suite to encourage reusability and reproducibility in science. Once published, their articles will feature a special widget linking to additional research output, such as raw, experimental repetitions, null or negative results, protocols and datasets.

A Reuse Recipe Document is a collection of additional research outputs, which could serve as a guidelines to another researcher trying to reproduce or build on the previously published work. In contrast to a research article, it is a dynamic ‘evolving’ research item, which can be later updated and also tracked back in time, thanks to a revision history feature.

Both the Recipe Document and the Reproducible Links, which connect subsequent outputs to the original publication, are assigned with their own DOIs, so that reuse instances can be easily captured, recognised, tracked and rewarded with increased citability.

With these events appearing on both the original author’s and any reuser’s ORCID, the former can easily gain further credibility for his/her work because of his/her work’s enhanced reproducibility, while the latter increases his/her own by showcasing how he/she has put what he/she has cited into use.

Furthermore, the transparency and interconnectivity between the separate works allow for promoting intra- and inter-disciplinary collaboration between researchers.

“At BDJ, we strongly encourage our authors to use CREDIT Suite to submit any additional research outputs that could help fellow scientists speed up progress in biodiversity knowledge through reproducibility and reusability,” says Prof. Lyubomir Penev, founder of the journal and its scholarly publisher – Pensoft. “Our new partnership with Profeza is in itself a sign that collaboration and integrity in academia is the way to good open science practices.”

“Our partnership with Pensoft is a great step towards gathering crucial feedback and insight concerning reproducibility and continuity in research. This is now possible with Reuse Recipe Documents, which allow for authors and reusers to engage and team up with each other,” says Sheevendra, Co-Founder of Profeza.

New ‘big-armed fly’ species named after former California governor Arnold Schwarzenegger

New species can be named for all types of attributes, but Natural History Museum of Los Angeles County entomologist Brian Brown knew exactly what name to give a bizarre new fly species he discovered in the Brazilian Amazon.

“As soon as I saw those bulging legs, I knew I had to name this one after Arnold,” says Brown. “Not only is he a major cultural icon and an important person in the political realm, his autobiography gave me some hope that I could improve my body as a skinny teenager.” For these reasons, Brown says, the former governor deserves to have the new fly named in his honor.

His research article is published in the open access Biodiversity Data Journal.

The fly is impressive in other ways, Brown explains. “It is known only from one female specimen that we almost overlooked because it is so incredibly small.”

In fact, it is the world’s smallest known fly, according to Brown, who should know, since he had previously described what was formerly the world’s smallest fly, at 0.400 mm in body length. The new fly, named Megapropodiphora arnoldi, is just a fraction smaller, coming in at 0.395 mm.

MegapropodiphoraHowever, unlike the enlarged forelegs that prompted the naming, the mid- and hind legs appear to be highly reduced, and the wings reduced to tiny stubs.

Even though the fly has not been observed in the wild, Brown concludes that it is clearly a parasitoid, probably of ants or termites, based on its pointed, sharp ovipositor. He further speculates that these flies probably grab onto the hosts and “hold on for dear life” until they reach a nest or colony where they can parasitize their victims more effectively.

Brown has had considerable success finding new species of tiny flies, which he says are “the continuing frontier for insect discovery.”

Some of the more obvious, larger insects might have already been described, but by looking at smaller specimens, especially from remote, tropical sites, the entomologist finds that almost everything is new.

Even in his home city of Los Angeles, Brown and collaborators found that almost half of the phorid flies were previously unknown.

For example, it was last year that they finally figured why a secretive fly had been observed around mushrooms with no clear explanation for nearly 30 years. The revelation occurred when L.A. Bed & Breakfast owners Patsy Carter and Lisa Carter-Davis decided to alert entomologists about a phenomenon happening in their yard.

Back in 2016, Brian and his team described at once a total of twelve scuttle fly species new to science after ‘field’ trips in the backyards of houses around the city of angels.

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Original source:

Citation: Brown B (2018) A second contender for “world’s smallest fly” (Diptera: Phoridae). Biodiversity Data Journal 6: e22396. https://doi.org/10.3897/BDJ.6.e22396