biodiversity informatics

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

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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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).

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.

Audit finds biodiversity data aggregators ‘lose and confuse’ data

In an effort to improve the quality of biodiversity records, the Atlas of Living Australia (ALA) and the Global Biodiversity Information Facility (GBIF) use automated data processing to check individual data items. The records are provided to the ALA and GBIF by museums, herbaria and other biodiversity data sources.

However, an independent analysis of such records reports that ALA and GBIF data processing also leads to data loss and unjustified changes in scientific names.

The study was carried out by Dr Robert Mesibov, an Australian millipede specialist who also works as a data auditor. Dr Mesibov checked around 800,000 records retrieved from the Australian Museum, Museums Victoria and the New Zealand Arthropod Collection. His results are published in the open access journal ZooKeys, and also archived in a public data repository.

“I was mainly interested in changes made by the aggregators to the genus and species names in the records,” said Dr Mesibov.

“I found that names in up to 1 in 5 records were changed, often because the aggregator couldn’t find the name in the look-up table it used.”

Another worrying result concerned type specimens – the reference specimens upon which scientific names are based. On a number of occasions, the aggregators were found to have replaced the name of a type specimen with a name tied to an entirely different type specimen.

The biggest surprise, according to Dr Mesibov, was the major disagreement on names between aggregators.

“There was very little agreement,” he explained. “One aggregator would change a name and the other wouldn’t, or would change it in a different way.”

Furthermore, dates, names and locality information were sometimes lost from records, mainly due to programming errors in the software used by aggregators to check data items. In some data fields the loss reached 100%, with no original data items surviving the processing.

“The lesson from this audit is that biodiversity data aggregation isn’t harmless,” said Dr Mesibov. “It can lose and confuse perfectly good data.”

“Users of aggregated data should always download both original and processed data items, and should check for data loss or modification, and for replacement of names,” he concluded.

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Original source:

Mesibov R (2018) An audit of some filtering effects in aggregated occurrence records. ZooKeys 751: 129-146. https://doi.org/10.3897/zookeys.751.24791

Dispatch from the field II: Students describe an elusive spider while stationed in Borneo

A mystery has long shrouded the orb-weaving spider genus Opadometa, where males and females belonging to one and the same species look nothing alike. Furthermore, the males appear to be so elusive that scientists still doubt whether both sexes are correctly linked to each other even in the best-known species.

Such is the case for Opadometa sarawakensis – a species known only from female specimens. While remarkable with their striking red and blue colors and large size, the females could not give the slightest hint about the likely appearance of the male Opadometa sarawakensis.

The red and blue female Opadometa sarawakensis — The red and blue female *Opadometa sarawakensis*

Nevertheless, students taking part in a recent two-week tropical ecology field course organized by the Naturalis Biodiversity Center and Leiden University, and hosted by the Danau Girang Field Centre (DGFC) on the island of Borneo, Malaysia, found a mature male spider hanging on the web of a red and blue female, later identified as Opadometa sarawakensis. Still quite striking, the male was colored in a blend of orange, gray, black, and silver.

At the brink of a long-awaited discovery and eager to describe the male, the students along with their lecturers and the field station scientific staff encountered a peril – with problematic species like the studied orb weaver they were in need for strong evidence to prove that it matched the female from the web. Furthermore, molecular DNA-based analysis was not an option at the time, since the necessary equipment was not available at DGFC.

On the other hand, being at the center of the action turned out to have advantages no less persuasive than DNA evidence. Having conducted thorough field surveys in the area, the team has concluded that the male’s observation on that particular female’s web in addition to the fact that no other Opadometa species were found in the area, was enough to prove they were indeed representatives of the same spider.

Adapting to the quite basic conditions at the DGFC laboratory, the students and their mentors put in use various items they had on hand, including smartphones paired up with headlights mounted on gooseneck clips in place of sophisticated cameras.

In the end, they gathered all the necessary data to prepare the formal description of the newly identified male.

Once they had the observations and the data, there was only one question left to answer. How could they proceed with the submission of a manuscript to a scholarly journal, so that their finding is formally announced and recognised?

Thanks to the elaborated and highly automated workflow available at the peer-reviewed open access Biodiversity Data Journal and its underlying ARPHA Writing Tool, the researchers managed to successfully compile their manuscript, including all underlying data, such as geolocations, and submit it from the field station. All in all, the authoring, peer review and publication – each step taking place within the ARPHA Platform‘s singular environment – took less than a month to complete. In fact, the paper was published within few days after being submitted.

This is the second publication in the series “Dispatch from the field”, resulting from an initiative led by spider taxonomist Dr Jeremy Miller. In 2014, another team of students and their mentors described a new species of curious one-millimetre-long spider from the Danau Girang Field Center. Both papers serve to showcase the feasibility of publication and sharing of easy to find, access and re-use biodiversity data.

“This has been a unique educational experience for the students,” says Jeremy. “They got to experience how tropical field biologists work, which is often from remote locations and without sophisticated equipment. This means that creativity and persistence are necessary to solve problems and complete a research objective. The fact that the students got to participate in advancing knowledge about this remarkable spider species by contributing to a manuscript was really exciting.”

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Original source:

Miller J, Freund C, Rambonnet L, Koets L, Barth N, van der Linden C, Geml J, Schilthuizen M, Burger R, Goossens B (2018) Dispatch from the field II: the mystery of the red and blue Opadometa male (Araneae, Tetragnathidae, Opadometa sarawakensis). Biodiversity Data Journal6: e24777. https://doi.org/10.3897/BDJ.6.e24777