In a world increasingly defined by data-driven decisions, biodiversity research stands to benefit from standardized and accessible data. Despite their importance for research, biodiversity datasets often fail to meet FAIR (Findable, Accessible, Interoperable, Reusable) standards, leading to concerns about data quality, reliability, and accessibility.
To address this, we propose a framework to retrieve, refine and align secondary biodiversity data with FAIR standards, utilizing the Darwin Core model. We followed four steps:
data localization (systematic review)
quality validation
standardization using the Darwin Core standard
sharing and archive in the appropriate repository.
Our approach integrates data validation and quality control steps to ensure that secondary data sets can be trusted.
Our study in Biodiversity Data Journalfocused on ecotonal estuarine ecosystems near the easternmost Amazon, where we recovered data from 46,000 individuals representing 3,871 taxa across eight biotic groups (birds, amphibians, reptiles, mammals, fish, phytoplankton, benthos, and plants) from 1985 to 2022. These data were used to illustrate how our strategy improves validation, making the data more reliable for macroecological modeling and conservation management. As data becomes more standardized, researchers around the world will be better equipped to collaborate, identify trends, protect ecosystems, and advance sustainability efforts.
Relationships between numbers of taxa and occurrences gathered through an extensive review of secondary biodiversity data from the Golfão Maranhense area, in the estuarine regions of eastern Amazonia.
Accessible biodiversity data empowers stakeholders and provides critical insights into ecosystem health and species conservation. However, without standardized formats, this data is often fragmented, incomplete, or difficult to compare. By creating a consistent framework for collecting, storing, and sharing data, we are opening the door to more informed decision-making and innovation in biodiversity conservation.
The key to conserving biodiversity is collaboration and transparency. By prioritizing accessible and standardized data, we ensure that vital information reaches those who need it most – whether it’s for scientific study, habitat management or policymaking.
Let’s continue to make biodiversity data a tool for global change!
Research article:
Marques N, Soares CDdeM, Casali DdeM, Guimarães E, Fava F, Abreu JMdaS, Moras L, Silva LGda, Matias R, Assis RLde, Fraga R, Almeida S, Lopes V, Oliveira V, Missagia R, Carvalho E, Carneiro N, Alves R, Souza-Filho P, Oliveira G, Miranda M, Tavares VdaC (2024) Retrieving biodiversity data from multiple sources: making secondary data standardised and accessible. Biodiversity Data Journal 12: e133775. https://doi.org/10.3897/BDJ.12.e133775
The beetle species Grebennikovius basilewskyi. Numbers next to arrows indicate patterns of phenotype statements explained in the section “Phenoscript: main patterns of phenotype statements”. Arrow numbers from T1 to T5 illustrate individual body parts. See more in the research study.
One of the most beautiful aspects of Nature is the endless variety of shapes, colours and behaviours exhibited by organisms. These traits help organisms survive and find mates, like how a male peacock’s colourful tail attracts females or his wings allow him to fly away from danger. Understanding traits is crucial for biologists, who study them to learn how organisms evolve and adapt to different environments.
To do this, scientists first need to describe these traits in words, like saying a peacock’s tail is “vibrant, iridescent, and ornate”. This approach works for small studies, but when looking at hundreds or even millions of different animals or plants, it’s impossible for the human brain to keep track of everything.
Computers could help, but not even the latest AI technology is able to grasp human language to the extent needed by biologists. This hampers research significantly because, although scientists can handle large volumes of DNA data, linking this information to physical traits is still very difficult.
To solve this problem, researchers from the Finnish Museum of Natural History, Giulio Montanaro and Sergei Tarasov, along with collaborators, have created a special language called Phenoscript. This language is designed to describe traits in a way that both humans and computers can understand. Describing traits with Phenoscript is like programming a computer code for how an organism looks.
Phenoscript uses something called semantic technology, which helps computers understand the meaning behind words, much like how modern search engines know the difference between the fruit “apple” and the tech company “Apple” based on the context of your search.
“This language is still being tested, but it shows a lot of promise. As more scientists start using Phenoscript, it will revolutionise biology by making vast amounts of trait data available for large-scale studies, boosting the emerging field of phenomics,”
explains Montanaro.
In their research article, newly published in the open-access, peer-reviewed Biodiversity Data Journal, the researchers make use of the new language for the first time, as they create semantic phenotypes for four species of dung beetles from the genus Grebennikovius. Then, to demonstrate the power of the semantic approach, they apply simple semantic queries to the generated phenotypic descriptions.
Finally, the team takes a look yet further ahead into modernising the way scientists work with species information. Their next aim is to integrate semantic species descriptions with the concept of nanopublications, “which encapsulates discrete pieces of information into a comprehensive knowledge graph”. As a result, data that has become part of this graph can be queried directly, thereby ensuring that it remains Findable, Accessible, Interoperable and Reusable (FAIR) through a variety of semantic resources.
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Research paper:
Montanaro G, Balhoff JP, Girón JC, Söderholm M, Tarasov S (2024) Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae). Biodiversity Data Journal 12: e121562. https://doi.org/10.3897/BDJ.12.e121562
What expert recommendations did the BiCIKL consortium give to policy makers and research funders to ensure that biodiversity data is FAIR, linked, open and, indeed, future-proof? Find out in the blog post summarising key lessons learnt from the Horizon 2020 project.
The publications so far include the grant proposal; conference abstracts, a workshop report, guidelines papers and deliverables submitted to the Commission.
The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially.
Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built workflow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.
Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes(RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs.
The publications so far also include the BiCIKL grant proposal, which earned the support of the European Commission in 2021; conference abstracts, submitted by the partners to two consecutive TDWG conferences; a project report that summarises recommendations on interoperability among infrastructures, as concluded from a hackathon organised by BiCIKL; and two Guidelines papers, aiming to trigger a culture change in the way data is shared, used and reused in the biodiversity field.
At the time of writing, the top three of the most read papers in the BiCIKL collection is completed by the grant proposal and the second Guidelines paper, where the partners – based on their extensive and versatile experience – present recommendations about the use of annotations and persistent identifiers in taxonomy and biodiversity publishing.
Access to data and services along the entire data and research life cycle in biodiversity science. The figure was featured in the BiCIKL grant proposal, now made available from the BiCIKL project collection in RIO Journal.
What one might find quite odd when browsing the BiCIKL collection is that each publication is marked with its own publication source, even though all contributions are clearly already accessible from RIO Journal.
This is because one of the unique features of RIOallows for consortia to use their project collection as a one-stop access point for all scientific results, regardless of their publication venue, by means of linking to the original source via metadata. Additionally, projects may also upload their documents in their original format and layout, thanks to the integration between RIO and ARPHA Preprints. This is in fact how BiCIKL chose to share their latest deliverables using the very same files they submitted to the Commission.
“In line with the mission of BiCIKL and our consortium’s dedication to FAIRness in science, we wanted to keep our project’s progress and results fully transparent and easily accessible and reusable to anyone, anywhere,”
explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.
“This is why we opted to collate the outcomes of BiCIKL in one place – starting from the grant proposal itself, and then progressively adding workshop reports, recommendations, research papers and what not. By the time BiCIKL concludes, not only will we be ready to refer back to any step along the way that we have just walked together, but also rest assured that what we have achieved and learnt remains at the fingertips of those we have done it for and those who come after them,” he adds.
The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”
The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft.
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 with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.
Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.
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 FAIR Data Place 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 biodiversity 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.
The Biodiversity Knowledge Hub is no longer existing on paper only! We are opening the 2nd day of the #BiCIKL_H2020 General Assembly looking at the prototype of the BKH created by the @LifeWatchERIC team. It's so exciting to see projects taking shape! 🤩 #Plovdivpic.twitter.com/RidzwBpxZx
“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,”
said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.
“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”
Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.
“The point is: do we want an integrated structure or do we prefer federated structures? 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.”
Joe Miller, Executive Secretary and Director at GBIF, commented:
“We are a brand new community, and we are in the middle of the growth process. 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 Biodiversity Knowledge Hub 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.”
Joana Pauperio (biodiversity curator at EMBL-EBI) atthe 2nd General Assembly of the BiCIKL project.
“BiCIKL is leading data infrastructure communities through some exciting and important developments”
said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (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 the 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.”
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 at the beginning of the next year.
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Learn more about BiCIKL on the project’s website at: bicikl-project.eu
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.
From 17th to 21st October 2022, the Biodiversity Information Standards (TDWG) conference – to be held in Sofia – will run under the theme “Stronger Together: Standards for linking biodiversity data”.
Between 17th and 21st October 2022, the Biodiversity Information Standards (TDWG) conference – to be held in Sofia, Bulgaria – will run under the theme “Stronger Together: Standards for linking biodiversity data”.
In addition to opening and closing plenaries, the conference will feature 14 symposia and a mix of other formats that include lightning talks, a workshop, and panel discussion, and contributed oral presentations and virtual posters.
For a seventh year in a row, all abstracts submitted to the annual conference are made publicly available in the dedicated TDWG journal: Biodiversity Information Science and Standards (BISS Journal).
Thus, the abstracts – published ahead of the event itself – are not only permanently and freely available in a ‘mini-paper’ format, but will also provide conference participants with a sneak peek into what’s coming at the much anticipated conference.
