Biodiversity Data Journal

Streamlined import of omics metadata from the European Nucleotide Archive (ENA) into an OMICS Data Paper manuscript

Pensoft creates a specialised data paper article type for the omics community within Biodiversity Data Journal to reflect the specific nature of omics data. The scholarly publisher and technology provider established a manuscript template to help standardise the description of such datasets and their most important features.

By Mariya Dimitrova, Raïssa Meyer, Pier Luigi Buttigieg, Lyubomir Penev

Data papers are scientific papers which describe a dataset rather than present and discuss research results. The concept was introduced to the biodiversity community by Chavan and Penev in 2011 as the result of a joint project of GBIF and Pensoft.

Since then, Pensoft has implemented the data paper in several of its journals (Fig. 1). The recognition gained through data papers is an important incentive for researchers and data managers to author better quality metadata and to make it Findable, Accessible, Interoperable and Re-usable (FAIR). High quality and FAIRness of (meta)data are promoted through providing peer review, data audit, permanent scientific record and citation credit as for any other scholarly publication. One can read more on the different types of data papers and how they help to achieve these goals in the Strategies and guidelines for scholarly publishing of biodiversity data (https://doi.org/10.3897/rio.3.e12431).

**Fig. 1** Number of data papers published in Pensoft’s journals since 2011.

The data paper concept was initially based on the standard metadata descriptions, using the Ecological Metadata Language (EML). Apart from distinguishing a specialised place for dataset descriptions by creating a data paper article type, Pensoft has developed multiple workflows for streamlined import of metadata from various repositories and their conversion into data paper a manuscripts in Pensoft’s ARPHA Writing Tool (AWT). You can read more about the EML workflow in this blog post.

Similarly, we decided to create a specialised data paper article type for the omics community within Pensoft’s Biodiversity Data Journal to reflect the specific nature of omics data. We established a manuscript template to help standardise the description of such datasets and their most important features. This initiative was supported in part by the IGNITE project.

How can authors publish omics data papers?

There are two ways to do publish omics data papers – (1) to write a data paper manuscript following the respective template in the ARPHA Writing Tool (AWT) or (2) to convert metadata describing a project or study deposited in EMBL-EBI’s European Nucleotide Archive (ENA) into a manuscript within the AWT.

The first method is straightforward but the second one deserves more attention. We focused on metadata published in ENA, which is part of the International Nucleotide Sequence Database Collaboration (INSDC) and synchronises its records with these of the other two members (DDBJ and NCBI). ENA is linked to the ArrayExpress and BioSamples databases, which describe sequencing experiments and samples, and follow the community-accepted metadata standards MINSEQE and MIxS. To auto populate a manuscript with a click of a button, authors can provide the accession number of the relevant ENA Study of Project and our workflow will automatically retrieve all metadata from ENA, as well as any available ArrayExpress or BioSamples records linked to it (Fig. 2). After that, authors can edit any of the article sections in the manuscript by filling in the relevant template fields or creating new sections, adding text, figures, citations and so on.

An important component of the OMICS data paper manuscript is a supplementary table containing MIxS-compliant metadata imported from BioSamples. When available, BioSamples metadata is automatically converted to a long table format and attached to the manuscript. The authors are not permitted to edit or delete it inside the ARPHA Writing Tool. Instead, if desired, they should correct the associated records in the sourced BioSamples database. We have implemented a feature allowing the automatic re-import of corrected BioSamples records inside the supplementary table. In this way, we ensure data integrity and provide a reliable and trusted source for accessing these metadata.

**Fig. 2** Automated generation of omics data paper manuscripts through import and conversion of metadata associated with the Project ID or Study ID at ENA

Here is a step-by-step guide for conversion of ENA metadata into a data paper manuscript:

The author has published a dataset to any of the INSDC databases. They copy its ENA Study or Project accession number.
The author goes to the Biodiversity Data Journal (BDJ) webpage, clicks the “Start a manuscript” buttоn and selects OMICS Data Paper template in the ARPHA Writing Tool (AWT). Alternatively, the author can also start from the AWT website, click “Create a manuscript”, and select “OMICS Data Paper” as the article type, the Biodiversity Data Journal will be automatically marked by the system. The author clicks the “Import a manuscript” button at the bottom of the webpage.
The author pastes the ENA Study or Project accession number inside the relevant text box (“Import an European Nucleotide Archive (ENA) Study ID or Project ID”) and clicks “Import”.
The Project or Study metadata is converted into an OMICS data paper manuscript along with the metadata from ArrayExpress and BioSamples if available. The author can start making changes to the manuscript, invite co-authors and then submit it for technical evaluation, peer review and publication.

For a detailed description of authoring an OMICS data paper, please refer to the Author Guidelines: https://bdj.pensoft.net/about#OmicsDataPapers

Our innovative workflow makes authoring omics data papers much easier and saves authors time and efforts when inserting metadata into the manuscript. It takes advantage of existing links between data repositories to unify biodiversity and omics knowledge into a single narrative. This workflow demonstrates the importance of standardisation and interoperability to integrate data and metadata from different scientific fields.

We have established a special collection for OMICS data papers in the Biodiversity Data Journal. Authors are invited to describe their omics datasets by using the novel streamlined workflow for creating a manuscript at a click of a button from metadata deposited in ENA or by following the template to create their manuscript via the non-automated route.

To stimulate omics data paper publishing, the first 10 papers will be published free of charge. Upon submission of an omics data paper manuscript, do not forget to assign it to the collection Next-generation publishing of omics data.

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.

Tiny fly from Los Angeles has a taste for crushed invasive snails

Living individual of Draparnaud’s glass snail
Photo by Kat Halsey

As part of their project BioSCAN – devoted to the exploration of the unknown insect diversity in and around the city of Los Angeles – the scientists at the Natural History Museum of Los Angeles County (USA) have already discovered numerous insects that are new to science, but they are still only guessing about the lifestyles of these species.

“Imagine trying to find a given 2 mm long fly in the environment and tracking its behavior: it is the smallest imaginable needle in the largest haystack. So when researchers discover new life histories, it is something worth celebrating,”
explains Dr. Brian Brown, lead author of a recent paper, published in the scholarly open-access Biodiversity Data Journal.

However, Brown and Maria Wong, former BioSCAN technician, while doing field work at the L.A. County Arboretum, were quick to reveal a curious peculiarity about one particular species discovered as part of the project a few years ago. They successfully lured female phorid flies by means of crushing tiny, invasive snails and using them as bait. In comparison, the majority of phorid flies, whose lifestyles have been observed, are parasitoids of social insects like ants.

Within mere seconds after the team crushed tiny invasive snails (Oxychilus draparnaudi), females representing the fly species Megaselia steptoeae arrived at the scene and busied themselves feeding. Brown and Wong then collected some and brought them home alive along with some dead snails. One of the flies even laid eggs. After hatching, the larvae were observed feeding upon the rotting snails and soon they developed to the pupal stage. However, none was reared to adulthood.

Female phorid fly feeding on a crushed Draparnaud’s glass snail
Photo by Kat Halsey

Interestingly, the host species – used by the fly to both feed on and lay eggs inside – commonly known as Draparnaud’s glass snail, is a European species that has been introduced into many parts of the world. Meanwhile, the studied fly is native to L.A. So far, it is unknown when and how the mollusc appeared on the menu of the insect.

To make things even more curious, species of other snail genera failed to attract the flies, which hints at a peculiar interaction worth of further study, point out the scientists behind the study, Brown and Jann Vendetti, curator of the NHM Malacology collection. They also hope to lure in other species of flies by crushing other species of snails.

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In recent years, the BioSCAN project led to other curious discoveries from L.A., also published in Biodiversity Data Journal. In 2016, a whole batch of twelve previously unknown scuttle fly species was described from the heart of the city. A year later, another mysterious phorid fly was caught ovipositing in mushroom caps after Bed & Breakfast owners called in entomologists to report on what they had been observing in their yard.

Original source:

Brown BV, Vendetti JE (2020) Megaselia steptoeae (Diptera: Phoridae): specialists on smashed snails. Biodiversity Data Journal 8: e50943. https://doi.org/10.3897/BDJ.8.e50943

Call for data papers from European Russia

Partners GBIF, FinBIF and Pensoft to support publication of data papers that describe datasets from Russia west of the Ural Mountains

Original post via GBIF

GBIF—the Global Biodiversity Information Facility—in collaboration with the Finnish Biodiversity Information Facility (FinBIF) and Pensoft Publishers, are happy to issue a call for authors to submit and publish data papers on European Russia (west of the Urals) in an upcoming special issue of Biodiversity Data Journal (BDJ).

Between now and 31 August 2020, the article processing fee (normally €450) will be waived for the first 20 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 31 August 2020. Late submissions will not be eligible for APC waivers.

Sponsorship is limited to the first 20 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 31 August. 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 2020. The journal is indexed by Web of Science (Impact Factor 1.029), Scopus (CiteScore: 1.24) 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 and b) appear in the paper’s list of references.

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.

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.

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.

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 European Russia west of the Ural mountains

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 European Russia west of the Ural mountains. However, authors of the paper may be affiliated with institutions anywhere in the world.

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Data audit at Pensoft’s biodiversity journals

Data papers submitted to Biodiversity Data Journal, as well as all relevant biodiversity-themed journals in Pensoft’s portfolio, undergo a mandatory data auditing workflow before being passed down to a subject editor.

Learn more about the workflow here:
https://www.eurekalert.org/pub_releases/2019-10/pp-aif101819.php.

Check out the case study below to see how the data audit workflow works in practice.

CASE STUDY: Data audit for the “Vascular plants dataset of the COFC herbarium (University of Cordoba, Spain)”, a data paper in PhytoKeys

Citizen scientists discover a new snail and name it after Greta Thunberg

A new to science species of land snail was discovered by a group of citizen scientists working together with scientists from Taxon Expeditions, a company that organises scientific field trips for teams consisting of both scientists and laypeople. Having conducted a vote on how to name the species, the expedition participants and the local staff of the National Park together decided to name the mollusc Craspedotropis gretathunbergae. The species name honors the young Swedish activist Greta Thunberg for her efforts to raise awareness about climate change. The study is published in the open-access journal Biodiversity Data Journal.

“The newly described snail belongs to the so-called caenogastropods, a group of land snails known to be sensitive to drought, temperature extremes and forest degradation”,
says snail expert and co-founder of Taxon Expeditions, Dr. Menno Schilthuizen.

All individuals were found very close to the research field station (Kuala Belalong Field Studies Centre) at the foot of a steep hill-slope, next to a river bank, while foraging at night on the green leaves of understorey plants.

Citizen scientist J.P. Lim, who found the first specimen of Greta Thunberg’s snail says:

“Naming this snail after Greta Thunberg is our way of acknowledging that her generation will be responsible for fixing problems that they did not create. And it’s a promise that people from all generations will join her to help”.

Taxon Expeditions participant J.P. Lim collecting snails.
*Credit:* Taxon Expeditions – Pierre Escoubas
*License: CC-BY 4.0*

The expedition team approached Ms. Thunberg who said that she would be “delighted” to have this species named after her.

Video about Taxon Expeditions & Greta Thunberg snail
Credit: Taxon Expeditions

However, this is not the first time that Taxon Expeditions team names a species in honour of an environmental advocate. In 2018, they named a new species of beetle after famous actor and climate activist Leonardo DiCaprio. Mr. DiCaprio temporarily changed his profile photo on Facebook to the photo of “his” beetle to acknowledge this honour.

View of the Ulu Temburong National Park in Brunei from the canopy bridge.
*Credit:* Taxon Expeditions – Pierre Escoubas
*License: CC-BY 4.0*

Original source:

Schilthuizen M, Lim JP, van Peursen ADP, Alfano M, Jenging AB, Cicuzza D, Escoubas A, Escoubas P, Grafe U, Ja J, Koomen P, Krotoski A, Lavezzari D, Lim L, Maarschall R, Slik F, Steele D, Ting Teck Wah D, van Zeeland I, Njunjić I (2020) Craspedotropis gretathunbergae, a new species of Cyclophoridae (Gastropoda: Caenogastropoda), discovered and described on a field course to Kuala Belalong rainforest, Brunei. Biodiversity Data Journal 8: e47484. https://doi.org/10.3897/BDJ.8.e47484

Fifteen years & 20 million insects later: Sweden’s impressive effort to document its insect fauna in a changing world

The Swedish Malaise Trap Project (SMTP) was launched in 2003 with the aim of making a complete list of the insect diversity of Sweden. Over the past fifteen years, an estimated total of 20 million insects, collected during the project, have been processed for scientific study. Recently, the team behind this effort published the resulting inventory in the open-access journal Biodiversity Data Journal. In their paper, they also document the project all the way from its inception to its current status by reporting on its background, organisation, methodology and logistics.

The SMTP deployed a total of 73 Malaise traps – a Swedish invention designed to capture flying insects – and placed them across the country, where they remained from 2003 to 2006. Subsequently, the samples were sorted by a dedicated team of staff, students and volunteers into over 300 groups of insects ready for further study by expert entomologists. At the present time, this material can be considered as a unique timestamp of the Swedish insect fauna and an invaluable source of baseline data, which is especially relevant as reports of terrifying insect declines keep on making the headlines across the world.

The first author and Project Manager of the SMTP, Dave Karlsson started his academic paper on the project’s results years ago by compiling various tips, tricks, lessons and stories that he had accumulated over his years as SMTP’s Project Manager. Some fun examples include the time when one of the Malaise traps was destroyed by a moose bull rubbing his antlers against it, or when another trap was attacked and eaten by a group of 20 reindeer. The project even had a trap taken out by Sweden’s military! Karlsson’s intention was that, by sharing the details of the project, he would inspire and encourage similar efforts around the globe.

Animals were not as kind to our traps as humans,” recall the scientists behind the project. One of the Malaise traps, located in the Brännbergets Nature Reserve in Västerbotten, was destroyed by a bull moose rubbing his antlers against it.
Photo by Anna Wenngren

Karlsson has worked with and trained dozens of workers in the SMTP lab over the past decade and a half. Some were paid staff, some were enthusiastic volunteers and a good number were researchers and students using SMTP material for projects and theses. Thus, he witnessed first-hand how much excitement and enthusiasm the work on insect samples under a microscope can generate, even in those who had been hesitant about “bugs” at first.

Stressing the benefits of traditional morphological approaches to inventory work, he says: “Appreciation for nature is something you miss when you go ‘hi-tech’ with inventory work. We have created a unique resource for specialists in our sorted material while fostering a passion for natural history.”

Sorted SMTP material is now available to specialists. Hundreds of thousands of specimens have already been handed over to experts, resulting in over 1,300 species newly added to the Swedish fauna. A total of 87 species have been recognised as new to science from the project thus far, while hundreds more await description.

The SMTP is part of the Swedish Taxonomy Initiative, from where it also receives its funding. In its turn, the latter is a project by the Swedish Species Information Center, a ground-breaking initiative funded by the Swedish Parliament since 2002 with the aim of documenting all multicellular life in Sweden.

The SMTP is based at Station Linné, a field station named after the famous Swedish naturalist and father of taxonomy, Carl Linneaus. Situated on the Baltic island of Öland, the station is managed by Dave Karlsson. Co-authors Emily Hartop and Mathias Jaschhof are also based at the station, while Mattias Forshage and Fredrik Ronquist (SMTP Project Co-Founder) are based at the Swedish Museum of Natural History.

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Original source:

Karlsson D, Hartop E, Forshage M, Jaschhof M, Ronquist F (2020) The Swedish Malaise Trap Project: A 15 Year Retrospective on a Countrywide Insect Inventory. Biodiversity Data Journal 8: e47255. https://doi.org/10.3897/BDJ.8.e47255

Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlazi, Pensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

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

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”

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Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

FAIR biodiversity data in Pensoft journals thanks to a routine data auditing workflow

*Data audit workflow provided for data papers submitted to Pensoft journals.*

To avoid publication of openly accessible, yet unusable datasets, fated to result in irreproducible and inoperable biological diversity research at some point down the road, Pensoft takes care for auditing data described in data paper manuscripts upon their submission to applicable journals in the publisher’s portfolio, including Biodiversity Data Journal, ZooKeys, PhytoKeys, MycoKeys and many others.

Once the dataset is clean and the paper is published, biodiversity data, such as taxa, occurrence records, observations, specimens and related information, become FAIR (findable, accessible, interoperable and reusable), so that they can be merged, reformatted and incorporated into novel and visionary projects, regardless of whether they are accessed by a human researcher or a data-mining computation.

As part of the pre-review technical evaluation of a data paper submitted to a Pensoft journal, the associated datasets are subjected to data audit meant to identify any issues that could make the data inoperable. This check is conducted regardless of whether the dataset are provided as supplementary material within the data paper manuscript or linked from the Global Biodiversity Information Facility (GBIF) or another external repository. The features that undergo the audit can be found in a data quality checklist made available from the website of each journal alongside key recommendations for submitting authors.

Once the check is complete, the submitting author receives an audit report providing improvement recommendations, similarly to the commentaries he/she would receive following the peer review stage of the data paper. In case there are major issues with the dataset, the data paper can be rejected prior to assignment to a subject editor, but resubmitted after the necessary corrections are applied. At this step, authors who have already published their data via an external repository are also reminded to correct those accordingly.

“It all started back in 2010, when we joined forces with GBIF on a quite advanced idea in the domain of biodiversity: a data paper workflow as a means to recognise both the scientific value of rich metadata and the efforts of the the data collectors and curators. Together we figured that those data could be published most efficiently as citable academic papers,” says Pensoft’s founder and Managing director Prof. Lyubomir Penev.

“From there, with the kind help and support of Dr Robert Mesibov, the concept evolved into a data audit workflow, meant to ‘proofread’ the data in those data papers the way a copy editor would go through the text,” he adds.

“The data auditing we do is not a check on whether a scientific name is properly spelled, or a bibliographic reference is correct, or a locality has the correct latitude and longitude”, explains Dr Mesibov. “Instead, we aim to ensure that there are no broken or duplicated records, disagreements between fields, misuses of the Darwin Core recommendations, or any of the many technical issues, such as character encoding errors, that can be an obstacle to data processing.”

At Pensoft, the publication of openly accessible, easy to access, find, re-use and archive data is seen as a crucial responsibility of researchers aiming to deliver high-quality and viable scientific output intended to stand the test of time and serve the public good.

CASE STUDY: Data audit for the “Vascular plants dataset of the COFC herbarium (University of Cordoba, Spain)”, a data paper in PhytoKeys

To explain how and why biodiversity data should be published in full compliance with the best (open) science practices, the team behind Pensoft and long-year collaborators published a guidelines paper, titled “Strategies and guidelines for scholarly publishing of biodiversity data” in the open science journal Research Ideas and Outcomes (RIO Journal).

Sir Charles Lyell’s historical fossils kept at London’s Natural History Museum accessible online

The Lyell Project team: First row, seated from left to right: Martha Richter (Principal Curator in Charge of Vertebrates), Consuelo Sendino (with white coat, curator of bryozoans holding a Lyell fossil gastropod from Canaries), Noel Morris (Scientific Associate of Invertebrates), Claire Mellish (Senior Curator of arthropods), Sandra Chapman (curator of reptiles) and Emma Bernard (curator of fishes, holding the lectotype of Cephalaspis lyelli). Second row, standing on from left to right: Jill Darrell (curator of cnidarians), Zoe Hughes (curator of brachiopods) and Kevin Webb (science photographer). Photo by Nelly Perez-Larvor.

More than 1,700 animal and plant specimens from the collection of eminent British geologist Sir Charles Lyell – known as the pioneer of modern geology – were organised, digitised and made openly accessible via the NHM Data Portal in a pilot project, led by Dr Consuelo Sendino, curator at the Department of Earth Sciences (Natural History Museum, London). They are described in a data paper published in the open-access Biodiversity Data Journal.

*Curator of plants Peta Hayes (left) and curator of bryozoans Consuelo Sendino (right) looking at a Lyell fossil plant from Madeira in the collection area. Photo by Mark Lewis.*

The records contain the data from the specimens’ labels (species name, geographical details, geological age and collection details), alongside high-resolution photographs, most of which were ‘stacked’ with the help of specialised software to re-create a 3D model.

Sir Charles Lyell’s fossil collection comprises a total of 1,735 specimens of fossil molluscs, filter-feeding moss animals and fish, as well as 51 more recent shells, including nine specimens originally collected by Charles Darwin from Tierra del Fuego or Galapagos, and later gifted to the geologist. The first specimen of the collection was deposited in distant 1846 by Charles Lyell himself, while the last one – in 1980 by one of his heirs.

With as much as 95% of the specimens having been found at the Macaronesian archipelagos of the Canaries and Madeira and dating to the Cenozoic era, the collection provides a key insight into the volcano formation and palaeontology of Macaronesia and the North Atlantic Ocean. By digitising the collection and making it easy to find and access for researchers from around the globe, the database is to serve as a stepping stone for studies in taxonomy, stratigraphy and volcanology at once.

*Sites where the Earth Sciences’ Lyell Collection specimens originate.*

“The display of this data virtually eliminates the need for specimen handling by researchers and will greatly speed up response time to collection enquiries,” explains Dr Sendino.

Furthermore, the pilot project and its workflow provide an invaluable example to future digitisation initiatives. In her data paper, Dr Sendino lists the limited resources she needed to complete the task in just over a year.

In terms of staff, the curator was joined by MSc student Teresa Máñez (University of Valencia, Spain) for six weeks while locating the specimens and collecting all the information about them; volunteer Jane Barnbrook, who re-boxed 1,500 specimens working one day per week for a year; NHM’s science photographer Kevin Webb and University of Lisbon’s researcher Carlos Góis-Marques, who imaged the specimens; and a research associate, who provided broad identification of the specimens, working one day per week for two months. Each of the curators for the collections, where the Lyell specimens were kept, helped Dr Sendino for less than a day. On the other hand, the additional costs comprised consumables such as plastazote, acid-free trays, archival pens, and archival paper for new labels.

“The success of this was due to advanced planning and resource tracking,” comments Dr Sendino.

“This is a good example of reduced cost for digitisation infrastructure creation maintaining a high public profile for digitisation,” she concludes.

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Original source:

Sendino C (2019) The Lyell Collection at the Earth Sciences Department, Natural History Museum, London (UK). Biodiversity Data Journal 7: e33504. https://doi.org/10.3897/BDJ.7.e33504

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About NHM Data Portal:

Committed to open access and open science, the Natural History Museum (London, UK) has launched the Data Portal to make its research and collections datasets available online. It allows anyone to explore, download and reuse the data for their own research.

The portal’s main dataset consists of specimens from the Museum’s collection database, with 4,224,171 records from the Museum’s Palaeontology, Mineralogy, Botany, Entomology and Zoology collections.

Citizen scientists discover pinhead-sized beetle in Borneo

The discovery is the latest in a series of newly described species collected as part of the Taxon Expeditions initiative aiming to bring biodiversity and taxonomy closer to the layperson

How many citizen scientists does it take to discover a new species? A recent expedition to the Ulu Temburong forest in Borneo proved that you only need 10 enthusiasts with no professional training, yet fueled with curiosity and passion for the outdoors, to find a new beetle the size of a pinhead in leaf litter.

*The newly discovered species of leaf beetle, Clavicornaltica belalongensis Photo by Taxon Expeditions – Pierre Escoubas.*

The species, named Clavicornaltica belalongensis, is a tiny, 1.25-mm-long leaf beetle that eats moss on the forest floor. Published in the open-access Biodiversity Data Journal, it is the latest discovery from Taxon Expeditions, an initiative that organises scientific field trips to remote and biodiverse locations for teams of scientists and laypeople.

*The Ulu Temburong forest, Borneo. Photo by Taxon Expeditions – Pierre Escoubas.*

Unlike other science/adventure trips, Taxon Expeditions gives a unique opportunity for laypeople, or citizen scientists, to describe and publish new species of animals and focus on the thousands of ‘little things that run the world’. Thanks to the initiative, they learn about tropical biology techniques while participating in the process of taxonomy and the study of hidden biodiversity.

The new beetle, for example, is one of hundreds of thousands of tiny beetle species that inhabit the leaf litter of tropical forests and have remained unknown and scientifically unnamed up to our days.

In a YouTube video, Simon Berenyi, who joined the expedition along with his 14-year-old son, says: ‘I had no idea how special this would be; you become a student again – you become a child again.’

Entomologist and founder of Taxon Expeditions, Dr. Iva Njunjić explains: ‘We introduce the general public to all these tiny, beautiful, and completely unknown animals, and show them that there is a whole world still to be discovered.’

Last year, another survey in Borneo organised by Taxon Expeditions ended up with the description of a new water beetle species (Grouvellinus leonardodicaprioi). Named after famous Hollywood actor and environmentalist Leonardo DiCaprio. The discovery raised a real furore on the public scene, culminating in the new insect making an appearance on the profile image of the celebrity’s facebook page.

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Original source:

Schilthuizen M, Berenyi A, Limin A, Brahim A, Cicuzza D, Eales A, Escoubas P, Grafe U, de Groot M, Hayden W, Paterno M, Jambul R, Slik J, Ting Teck Wah D, Tucker A, Njunjić I (2019) A new species of Clavicornaltica (Coleoptera: Chrysomelidae), discovered and described on a field course to Kuala Belalong, Brunei. Biodiversity Data Journal 7: e32555. https://doi.org/10.3897/BDJ.7.e32555