Linking FAIR biodiversity data, NEW article collection in BDJ

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

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

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

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

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

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

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

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

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

Conditions for publication and types of articles:

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


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

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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

Species conservation profile of a critically endangered endemic for the Azores spider

Subject to continuing population decline due to a number of factors, an exclusively cave-dwelling (troglobitic) spider endemic to the Azores is considered as Critically Endangered according to the IUCN Red List criteria.

To provide a fast output, potentially benefiting the arachnid’s survival, scientists from the IUCN – Spider and Scorpion Specialist Group and the Azorean Biodiversity Group (cE3c) at University of Azores, where the main objective is to perform research that addresses societal challenges in ecology, evolution and the environment, also known as the three E’s from the centre’s name abbreviation, teamed up with colleagues from University of Barcelona, Spain, and the Finnish Museum of Natural History.

Together, they make use of a specialised novel publication type feature, called Species Conservation Profile, created by the open access journal Biodiversity Data Journal, to provide scholarly credit and citation for the IUCN Red List species page, as well as pinpoint the population trends and the reasons behind them.

The studied spider species (scientifically called Turinyphia cavernicola) is a pale creature with long legs, large eyes and a total size of merely 2 mm in length. These spiders never leave their underground habitats, which are strictly humid lava tubes and volcanic pits. There they build sheet webs in small holes and crevices on the walls of the caves.

The volcanic pit Algar do Carvão (Terceira, Azores), the main location of the species Turyniphia cavernicola.Not only is the species restricted to a single island within the Azorean archipelago (Portugal), but it is only found in three caves. Furthermore, out of the three, only one of them is home to a sustainable large population. These caves are under severe threat due to pasture intensification, road construction and tourist activities.

Although there is not much information about the species distribution through the years, with the spider having been discovered as recently as in 2008, the authors make the assumption that originally there have been significantly greater populations. Not only have they studied thoroughly another fifteen caves located on the island without finding any individuals, but they have identified increasing anthropogenic impact on the habitat.

“The species original distribution was potentially very large compared with the current,” the scientists explain. “Relatively intensive searches in and around the current caves where the species occurs have failed to find additional subpopulations.”

“The trend of decline is based on the assumption that this species can occur in all these caves and that the absence is due to anthropogenic disturbance on caves during the last 50 years,” they note.

 

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Original source:

Borges P, Crespo L, Cardoso P (2016) Species conservation profile of the cave spiderTurinyphia cavernicola (Araneae, Linyphiidae) from Terceira Island, Azores, Portugal.Biodiversity Data Journal 4: e10274. doi: 10.3897/BDJ.4.e10274