After three years of advancing a cultural shift in identifying, linking, integrating, and re-using biodiversity data throughout the research cycle, the BiCIKL project is coming to a close.
One of the key outputs of the BiCIKL project is the Biodiversity Knowledge Hub (BKH). Developed as a one-stop portal for understanding the interconnected landscape of European biodiversity research infrastructures, it acts as a knowledge broker for users who want to navigate and access open and FAIR biodiversity data, guidelines, tools, and services.
Additionally, the BiCIKL project’s partners created training materials and detailed instructions to help users make the most of the linked services and access biodiversity data found in published literature. The training resources are divided into three courses to cater to users with different backgrounds and expertise, enabling them to begin with the fundamentals or concentrate on specific modules as required:
The Introduction to BKH coursepresents the BKH portal and helps users understand the functions offered by BKH and its associated data services.
The BKH Services course provides an overview of the services available in the BKH, and explains how to use each of them, with each service having its dedicated module, and offering best practices and recommendations for their use.
The Data Liberation and Publishing Tools Course is an advanced training course focusing on a more in-depth version of the multiple services featured on the BKH. This detailed module focuses on data liberation and publishing tools.
The courses, fully open and accessible to everyone, offer training materials that benefit various stakeholders. Research institutions can learn how different research infrastructures connect their data and add value for new user communities. Biodiversity researchers can explore new data sources, reduce errors in taxonomic name usage, and conduct complex queries. Taxonomists can compare name usage across checklists, access newly published information on a taxon, and create custom taxonomies. Biodiversity informaticians can discover data links, access guidance on identifiers and APIs, and compile complex datasets. Managers of biological collections can understand how their data is utilized and access linked data such as taxon names and sequences. Additionally, publishers can obtain guidelines, best practices, and tools for semantic publishing and implement persistent identifiers and workflows for Linked Open Data.
LifeWatch ERIC, via its Training Platform, will continue to host publicly accessible training materials even after the project’s conclusion, thus ensuring their long term sustainability. To learn more, please visit our Training Platform: https://training.lifewatch.eu/international-projects/resources/?category=32
The Horizon 2020 BiCIKL Project, of which LifeWatch ERIC is partner, announces that the Biodiversity Knowledge Hub(BKH) is now online.
The BKH is a one-stop portal that allows users to access FAIR and interlinked biodiversity data and services in a few clicks. BKH has been designed to support a new emerging community of users over time and across the entire biodiversity research cycle providing its services to anybody, anywhere and anytime.
“We have invested our best energies and resources in the development of BKH and the Fair Data Place (FDP), which is the beating heart of the portal” – says Christos Arvanitidis, CEO of LifeWatch ERIC – “BKH has been designed to support a new emerging community of users across the entire biodiversity research cycle. Its purpose goes beyond the BiCIKL project itself: we are thrilled to say that BKH is meant to stay, aiming to reshape the way biodiversity knowledge is accessed and used.”
The BKH is designed to serve a new emerging community of users over time and across the entire biodiversity research cycle.
“The Knowledge Hub is the main product from our BiCIKL consortium, and we are delighted with the result! BKH can easily be seen as the beginning of the major shift in the way we search interlinked biodiversity information,” says Prof. Lyubomir Penev, BiCIKL’s Project coordinator and Founder of Pensoft Publishers.
“Biodiversity researchers, research infrastructures and publishers interested in fields ranging from taxonomy to ecology and bioinformatics can now freely use BKH as a compass to navigate the oceans of biodiversity data. BKH will do the linkages,” he adds.
“The BKH outlines how users can navigate and access the linked data, tools and services of the infrastructures cooperating in BiCIKL,” said Joe Miller, Executive Secretary of GBIF—the Global Biodiversity Information Facility. “By revealing how they harvest, liberate and reuse data, these increasingly integrated sources enable researchers in the natural sciences to move more seamlessly between specimens and material samples, genomic and metagenomic data, scientific literature, and taxonomic names and units.”
The Horizon 2020 – funded Project BiCIKL, in which LifeWatch ERIC is a partner, has reached its halfway stage. The partners gathered in Plovdiv(Bulgaria) from 22 – 25 October for the Second General Assembly, brilliantly organised by Pensoft Publishers.
The BiCIKL project will launch a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services. BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.
BiCIKL is keeping pace as expected (16 out of 48 deliverables have been submitted, 9 are in progress/under review and due in a few days, 21 out of 48 milestones have been achieved).
The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable). This online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.
This data includes information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.
Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.
Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.
By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.
“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few. I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world” – said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft, a scholarly publisher and technology provider company.
“The point is: do we want an integrated structure or do we prefer federated structures?” – says Christos Arvanitidis, LifeWatch ERIC – “What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”
“We are a brand new community, and we are in the middle of the growth process” – says Joe Miller, GBIF– “We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the BKH is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”
“BiCIKL is leading data infrastructure communities through some exciting and important developments”, says Guy Cochrane, EMBL-EBI. “In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge.”
“As a partner, we, at Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge”, says Deborah Paul, chair of the Biodiversity Information Standards-TDWG.
The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded (https://bicikl-project.eu/open-call-projects) at the beginning of the next year.
To learn more about projects in which LifeWatch ERIC is involved, please visit our Related Projects page.
The BiCIKL project is welcoming submissions of Expression of Interest (EoI) for 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 up the BiCIKL project.
BiCIKL has established 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.
To learn more about this Open Call for Projects, please visit the dedicated page on the BiCIKL project website.
You can learn more about the projects LifeWatch ERIC is involved in on the Related Projects page.
The fourteen partners of the BiCIKL Project met in Seville (Spain) for their first physical meeting at the beginning of May, one year after the start of the project, whose mission is to catalyse a top-down culture change in the way researchers work with data about the world’s biodiversity at each step of the research process.
“We will cultivate a more transparent, trustworthy and efficient research ecosystem,” were among the words to remember from the meeting’s opening, summarising the rationale behind BiCIKL.
Hosted by LifeWatch ERIC, the event at La Casa de la Ciencia provided fertile ground for new ideas, as partners spent three days together discussing and analysing how their tools, workflows and platforms have evolved during the past year – and their next steps toward improvements in retrieving, preserving and linking different sources of biodiversity data.
The meeting had a strong technical focus on the transition from one-sided, uni-directional linkages between biodiversity data and infrastructures to more complex bilateral and multi-directional connections across various types of FAIR and open data.
So far, such links are mainly possible within the scientific publishing process, but that’s going to change.
“What researchers and research infrastructures would find particularly useful and enjoyable is that – as a result of our joint efforts at BiCIKL – scientific literature will become an integral part of the biodiversity research lifecycle,” said Prof Lyubomir Penev, BiCIKL’s Project Coordinator, founder and CEO of Pensoft Publishers. “We are working on several workflows and tools that continue to facilitate the biodiversity publishing of the future even after the project’s end.”
“The most important outcome of this meeting is the return of the BiCIKL community vis-à-vis”, the Partners say, without forgetting what will be next, “Much of the knowledge about biodiversity is largely imprisoned in an ever-growing corpus of 500 million pages of scientific research publications. We are trying to liberate that information as data, make it permanently available from the Biodiversity Literature Repository, and improve international standards and practices more broadly. We include adequate support text, answering questions about biodiversity and data mining applications.
One year after the debut of the BiCIKL Project, partners and research infrastructures will meet all together in person for the first time. A three-day of presentation of the tasks completed, bilateral meetings and technical forums will take place in Seville (Spain) between 2 – 4 May 2022.
“We are all thrilled about this convention,” Project Coordinator Prof Lyubomir Penev comments. “It is going to be a huge step forward and an important moment for planning the activities to come.”
During the meeting, which will be held at La Casa de la Ciencia, Seville, LifeWatch ERIC and GBIF will be presenting The Biodiversity Knowledge Hub (BKH), a structure at the core of the BiCIKL Project.
“We can’t reveal much before the meeting,” – says Christos Arvanitidis, LifeWatch ERIC CEO, “but BKH will be a single knowledge portal that helps researchers access and use interlinked and machine-readable FAIR data (Findable, Accessible, Interoperable and Reusable) relying on unique stable identifiers on specimens, genomics, observations, taxonomy and data in publications.”
There will be much more in the Andalusian venue: technical discussions will take place on linking between data classes, for instance, and the event will be wrapped up with a Forum on the BKH and the Fair Data Place.
We invite all biodiversity scientists to fill in this survey, which aims to identify gaps and trends in the ways in which biodiversity scientists access and use data in their research, by asking participants to describe use cases from their previous or projected work experience. The most appealing use cases will be invited to the open call for Trans-national access projects supported by the BiCIKL project.
BiCIKL is an EU project that aims to provide access and tools for seamless linking between the data along the biodiversity research cycle: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use. BiCIKL will develop and implement new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature.
In a recently started Horizon 2020-funded project, 15 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. LifeWatch ERIC is one of these institutions. By linking their technologies, these project partners 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.
The kick-off meeting for the Biodiversity Community Integrated Knowledge Library (BiCIKL) took place last week on 27-28 May! LifeWatch ERIC is proud to be one of the fourteen official partners of this Horizon 2020 project,* contributing to the establishment of open science practices in the biodiversity domain as it follows its own mission to become a worldwide provider of content and services for this research community.
But what is BiCIKL?
BiCIKL is an EU-funded project coordinated by Pensoft that aims to unite key European and international research infrastructures across ten countries in their quest to facilitate open science and fair data practices in the biodiversity scientific community. Its four key products have been identified as: a community equipped with tools for searching and accessing FAIR (findable, accessible, interoperable, and reusable) interlinked data; an interlinked corpora of knowledge for biodiversity and related research domains; automated tools and workflows for data liberation and FAIRisation from literature; and semantic-based journal production workflows for publication and reuse of FAIR biodiversity data.
What exactly does it do?
BiCIKL plans to build a Biodiversity Knowledge Hub, providing access to data, associated tools and services at each stage and along the entire research cycle. Speaking technically, it will focus on harvesting, liberating, linking and reusing subarticle level data literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables, etc.), whether PDF- or XML-based. It will provide seamless linking and usage tracking of data along the line: specimens → sequences → species → analytics → publications → biodiversity knowledge graph → re-use.
What role does LifeWatch ERIC play?
LifeWatch ERIC, which already carries out specialised work in the areas of semantics and usage tracking, will be key in helping BiCIKL develop the methods, tools and workflows required for the realisation of BiCIKL goals. Its two main tasks will be to analyse the technical requirement of users and implement the Biodiversity Knowledge Hub (BiKH). It will participate in testing and streamlining interoperability and the alignment of findability, reuse and accessibility. Furthermore, LifeWatch ERIC will contribute to defining and implementing the necessary operational framework, as well as identifying BiKH components and translating the functional diagramme and operational framework into an educational cloud.
BiCIKL’s website is currently under construction, but you can follow its activities on Twitter.
*grant agreement No. 101007492, duration May 2021-2024
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The Spanish National Distributed Centre is supported by the Ministry of Science, Innovation and Universities, the Regional Government of Andalusia and the Guadalquivir River Basin Authority (Ministry for Ecological Transition-MITECO). Moreover, Spain is the hosting Member State of LifeWatch ERIC, the location of its Statutory Seat & ICT e-Infrastructure Technical Office (LifeWatch ERIC Common Facilities).
To know more about how Spain contributes to LifeWatch ERIC, please visit our dedicated webpage.
The Slovenian National Distributed Centre is led by the Research Centre of the Slovenian Academy of Sciences and Arts (ZRC SAZU). It focuses on the development of technological solutions in the field of biodiversity and socio-ecosystem research.
To know more about how Slovenia contributes to LifeWatch ERIC, please visit our dedicated webpage.
The Portuguese National Distributed Centre is managed by PORBIOTA, the Portuguese e-Infrastructure for Information and Research on Biodiversity. Led by BIOPOLIS/CIBIO-InBIO – Research Centre in Biodiversity and Genetic Resources, PORBIOTA connects the principal Portuguese research institutions working in biodiversity.
To know more about how Portugal contributes to LifeWatch ERIC, please visit our dedicated webpage.
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The Italian National Distributed Centre is led and managed by the Italian National Research Council (CNR) and is coordinated by a Joint Research Unit, currently comprising 35 members. Moreover, Italy hosts one of the LifeWatch ERIC Common Facilities, the Service Centre.
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The Belgian National Distributed Centre makes varied and complementary in-kind contributions to LifeWatch ERIC. These are implemented in the form of long-lasting projects by various research centres and universities distributed throughout the country and supported by each respective political authority.
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