Guidelines for scholarly publishing of biodiversity data from Pensoft and EU BON

While development and implementation of data publishing and sharing practices and tools have long been among the core activities of the academic publisher Pensoft, it is well-understood that as part of scholarly publishing, open data practices are also currently in transition, and hence, require a lot of collaborative and consistent efforts to establish.

Based on Pensoft’s experience, and elaborated and updated during the Framework Program 7 EU BON project, a new paper published in the EU BON dedicated collection in the open science journal Research Ideas and Outcomes (RIO), outlines policies and guidelines for scholarly publishing of biodiversity and biodiversity-related data. Newly accumulated knowledge from large-scale international efforts, such as FORCE11 (Future of Research Communication and e-Scholarship), CODATA (The Committee on Data for Science and Technology), RDA (Research Data Alliance) and others, is also included in the Guidelines.

The present paper discusses some general concepts, including a definition of datasets, incentives to publish data and licences for data publishing. Furthermore, it defines and compares several routes for data publishing, namely: providing supplementary files to research articles; uploading them on specialised open data repositories, where they are linked to the research article; publishing standalone data papers; or making use of integrated narrative and data publishing through online import/download of data into/from manuscripts, such as the workflow provided by the Biodiversity Data Journal. Among the guidelines, there are also comprehensive instructions on preparation and peer review of data intended for publication.

Although currently available for journals using the developed by Pensoft journal publishing platform ARPHA, these strategies and guidelines could be of use for anyone interested in biodiversity data publishing.

Apart from paving the way for a whole new approach in data publishing, the present paper is also a fine example of science done in the open, having been published along with its two pre-submission public peer reviews. The reviews by Drs. Robert Mesibov and Florian Wetzel are both citable via their own Digital Object Identifiers (DOIs).


Original source:

Penev L, Mietchen D, Chavan V, Hagedorn G, Smith V, Shotton D, Ó Tuama É, Senderov V, Georgiev T, Stoev P, Groom Q, Remsen D, Edmunds S (2017) Strategies and guidelines for scholarly publishing of biodiversity data. Research Ideas and Outcomes 3: e12431.

Novel genetic tools for bioassessment of European aquatic ecosystems, COST grant proposal

Often referred to as “the blue planet”, the majority of the Earth consists of aquatic ecosystems. Human land-use change, over-exploitation and pollution have severely impacted aquatic ecosystems over the past decades.

In order to protect and maintain central ecosystem services obtained from aquatic ecosystems, such as clean water and food, conservation actions have been proposed in order to protect and preserve our planet’s water ecosystems. Bioassessment and continuous monitoring are the central tools to evaluate the success of conservation management actions. However they are not efficient enough at the moment.

The DNAqua-Net project, funded under the European framework COST, is set to gather a large international professional community from across disciplines and fields in order to develop best practice strategies for using novel genetic tools in real-world bioassessment and monitoring of aquatic ecosystems in Europe and beyond. The grant proposal, authored by a large international team, is published in the open access journal Research Ideas and Outcomes (RIO).

Currently, biodiversity assessment relies on morpho-taxonomy, meaning species are identified based on studying the morphology of collected and manually sorted specimens. However, this approach is largely flawed due to being time-consuming, limited in temporal and spatial resolution, and dependent on the varying individual taxonomic expertise of the analysts.

In contrast, novel genomic tools, meant to be researched and developed over the course of DNAqua-Net, offer new solutions. They rely on DNA barcoding to identify species, even those undescribed yet, and assess biodiversity of water ecosystems using standardised genetic markers.

DNA barcoding is a modern taxonomic tool, which uses short standardised gene fragments of organisms allowing an unequivocal assignment to species level based on sequence data. Standardised DNA-barcode libraries, generated by the international Barcode of Life project (iBOL), and its associated and validated databases, such as BOLD and R-Syst provide reference data, which make it possible to analyse multiple environmental samples within a few days.

So far, a major problem in developing and adopting genomic tools has been that scientists have been working independently in different institutions rather unconnected from end-users. However, the DNAqua-Net team’s aim is to establish a cross-discipline, international network of scientists, managers, governmental institutions, manufacturers, and emerging service providers. Together, they would be able to identify the challenges in DNA-based bioassessment and provide standardised best-practice solutions.

Furthermore, as technological progress continues, DNA does not have to be necessarily extracted from tissue, but can also be collected from sediments, biofilms, or the water itself. Also called ‘environmental DNA’ (eDNA), it can provide information on much more than a number of specifically targeted species. Instead, it could deliver data on the entire biodiversity of micro-, meio- and macro-organisms living in an aquatic environment. While being far less invasive than traditional sampling techniques, the combined eDNA metabarcoding approach could also detect alien species and thus, act as an early warning for management.

“Novel DNA-based approaches currently emerge, possibly acting as a “game-changer” in environmental diagnostics and bioassessments by providing high-resolution pictures of biodiversity from micro to macro scales,” comment the authors.


Original source:

Leese F, Altermatt F, Bouchez A, Ekrem T, Hering D, Meissner K, Mergen P, Pawlowski J, Piggott J, Rimet F, Steinke D, Taberlet P, Weigand A, Abarenkov K, Beja P, Bervoets L, Björnsdóttir S, Boets P, Boggero A, Bones A, Borja Á, Bruce K, Bursi? V, Carlsson J, ?iampor F, ?iamporová-Zatovičová Z, Coissac E, Costa F, Costache M, Creer S, Csabai Z, Deiner K, DelValls Á, Drakare S, Duarte S, Eleršek T, Fazi S, Fišer C, Flot J, Fonseca V, Fontaneto D, Grabowski M, Graf W, Guðbrandsson J, Hellström M, Hershkovitz Y, Hollingsworth P, Japoshvili B, Jones J, Kahlert M, Kalamujic Stroil B, Kasapidis P, Kelly M, Kelly-Quinn M, Keskin E, Kõljalg U, Ljubeši? Z, Maček I, Mächler E, Mahon A, Marečková M, Mejdandzic M, Mircheva G, Montagna M, Moritz C, Mulk V, Naumoski A, Navodaru I, Padisák J, Pálsson S, Panksep K, Penev L, Petrusek A, Pfannkuchen M, Primmer C, Rinkevich B, Rotter A, Schmidt-Kloiber A, Segurado P, Speksnijder A, Stoev P, Strand M, Šulčius S, Sundberg P, Traugott M, Tsigenopoulos C, Turon X, Valentini A, van der Hoorn B, Várbíró G, Vasquez Hadjilyra M, Viguri J, Vitonyt? I, Vogler A, Vrålstad T, Wägele W, Wenne R, Winding A, Woodward G, Zegura B, Zimmermann J (2016) DNAqua-Net: Developing new genetic tools for bioassessment and monitoring of aquatic ecosystems in Europe. Research Ideas and Outcomes 2: e11321.

Scattered marine cave biodiversity data to find home in new database WoRCS, Project Report

Considered “biodiversity reservoirs,” underwater caves are yet to be explored with only a few thoroughly researched areas in the world. Furthermore, species diversity and distributional data is currently scattered enough to seriously hinder conservation status assessments, which is of urgent need due to planned and uncontrolled coastal urbanization.

Thereby, a large international team of scientists, led by Dr Vasilis Gerovasileiou, Hellenic Centre for Marine Research, Greece, have undertaken the World Register of marine Cave Species (WoRCS) initiative meant to aggregate ecological and geographical data to eventually provide information vital for evidence-based conservation. Their Project Report is published in the open access journal Research Ideas and Outcomes (RIO).

With more than 20,000 existing records of underwater cave-dwelling species spread across several platforms, the authors have identified the need for a new database, where a standard glossary based on existing terminology binds together all available ecological data, such as type of environment, salinity regimes, and cave zone, as well as geographical information on the distribution of species in these habitats.

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In their project, which has already produced a dynamic webpage, the scientists work within the context of the World Register of Marine Species (WoRMS) to add the already available records published in peer-reviewed outlets to reliable and case-by-case verified unpublished data, available from offline databases, museum collections and field notes, as well as the findings of the WoRCS thematic editors themselves.

Eventually, these presence records could be georeferenced for submission to the Ocean Biogeographic Information System (OBIS) and constitute an important dataset for biogeographical and climate change studies on marine caves and anchialine systems.

To invite both the marine biology scientific communities and citizen scientists, WoRCS is meant to adopt a number of strategies.

Short and mid-term plans to engage the scientific community include development of common projects on poorly known marine and anchialine caves; projects that use WoRCS data; initiation of a fellowship programme to engage young researchers; and work with societies.

In the meantime, WoRCS is also intended to develop educational, citizen science and conservation activities, by creating products (e.g., maps, guides, courses) for the public, engage volunteers to encode data, and develop tools for MPA managers and the conservationist community.

“In particular, each time that a project about caves is funded, a work package or module or deliverable about WoRCS should be included to employ students and young researchers for data encoding, or to facilitate new types of data, or new links to other e-infrastructures and data tools,” suggest the WoRCS thematic editors.


Original source:

Gerovasileiou V, Martínez A, Álvarez F, Boxshall G, Humphreys W, Jaume D, Becking L, Muricy G, van Hengstum P, Dekeyzer S, Decock W, Vanhoorne B, Vandepitte L, Bailly N, Iliffe T (2016) World Register of marine Cave Species (WoRCS): a new Thematic Species Database for marine and anchialine cave biodiversity. Research Ideas and Outcomes 2: e10451. doi:10.3897/rio.2.e10451