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 Expression of Interest for biodiversity data-related scientific projects from BiCIKL

The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.

The BiCIKL project invites submissions of Expression of Interest (EoI) to the First BiCIKL Open Call for projects. The purpose of this call is to solicit, select and implement four to six biodiversity data-related scientific projects that will make use of the added value services developed by the leading Research Infrastructures that make the BiCIKL project.

By opening this call, BiCIKL aims to better understand how it could support scientific questions that arise from across the biodiversity world in the future, while addressing specific scientific or technical biodiversity data challenges presented by the applicants.

We need and want to assess real-world problems and make the best possible use of our data and technical capabilities. This will greatly assist in defining the long-term development goals of the participating Research Infrastructures and improve the way they can technically and operationally work together to deliver greater scientific value.

explain the project partners.

The BiCIKL project – a Horizon 2020-funded project involving 14 European institutions, representing major global players in biodiversity research and natural history, and coordinated by Pensoft – establishes a European starting community of key research infrastructures, researchers, citizen scientists and other biodiversity and life sciences stakeholders based on open science practices through access to data, tools and services.

Find more about the Call and submit your Expression of Interest

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New BiCIKL project to build a freeway between pieces of biodiversity knowledge

The new Horizon 2020-funded project BiCIKL (Biodiversity Community Integrated Knowledge Library) is a partnership of 14 European institutions, representing the continent’s and global key players in biodiversity research and data. They have committed to link their infrastructures and technologies, in order to provide flawless access to data across all stages of the research process. Three years in, BiCIKL will have created the first-of-its-kind Biodiversity Knowledge Hub.

In a recently started Horizon 2020-funded project, 14 European institutions from 10 countries, representing both the continent’s and global key players in biodiversity research and natural history, deploy and improve their own and partnering infrastructures to bridge gaps between each other’s biodiversity data types and classes. By linking their technologies, they are set to provide flawless access to data across all stages of the research cycle.

Three years in, BiCIKL (abbreviation for Biodiversity Community Integrated Knowledge Library) will have created the first-of-its-kind Biodiversity Knowledge Hub, where a researcher will be able to retrieve a full set of linked and open biodiversity data, thereby accessing the complete story behind an organism of interest: its name, genetics, occurrences, natural history, as well as authors and publications mentioning any of those.

Ultimately, the project’s products will solidify Open Science and FAIR (Findable, Accessible, Interoperable and Reusable) data practices by empowering and streamlining biodiversity research.

Together, the project partners will redesign the way biodiversity data is found, linked, integrated and re-used across the research cycle. By the end of the project, BiCIKL will provide the community with a more transparent, trustworthy and efficient highly automated research ecosystem, allowing for scientists to access, explore and put into further use a wide range of data with only a few clicks.

“In recent years, we’ve made huge progress on how biodiversity data is located, accessed, shared, extracted and preserved, thanks to a vast array of digital platforms, tools and projects looking after the different types of data, such as natural history specimens, species descriptions, images, occurrence records and genomics data, to name a few. However, we’re still missing an interconnected and user-friendly environment to pull all those pieces of knowledge together. Within BiCIKL, we all agree that it’s only after we puzzle out how to best bridge our existing infrastructures and the information they are continuously sourcing that future researchers will be able to realise their full potential,” 

explains BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft, a scholarly publisher and technology provider company.

Continuously fed with data sourced by the partnering institutions and their infrastructures, BiCIKL’s key final output: the Biodiversity Knowledge Hub, is set to persist with time long after the project has concluded. On the contrary, by accelerating biodiversity research that builds on – rather than duplicates – existing knowledge, it will in fact be providing access to exponentially growing contextualised biodiversity data.

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Learn more about BiCIKL on the project’s website at: bicikl-project.eu

Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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The project partners: