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The Global Biodiversity Portal: enabling biodiversity research worldwide

The new initiative brings together genomic data from various biodiversity projects to aid conservation and biodiversity efforts

The Global Biodiversity Data Portal. Credit: Karen Arnott/EMBL-EBI

Summary

  • The Global Biodiversity Portal is a centralised open-access database that consolidates genomic information collected from projects that make up the Earth BioGenome Project, aiding conservation and biodiversity efforts

  • The portal offers user-friendly search filters and features including sequencing status tracking

  • Designed for scalability and regular updates, the portal harmonises data from diverse sources and keeps information current for emerging global biodiversity initiatives

EMBL’s European Bioinformatics Institute (EMBL-EBI) has launched the Global Biodiversity Portal – an open access data portal that will consolidate genomic information from different biodiversity projects within the Earth BioGenome Project.


Sequencing and storing the genomic data of all species on Earth is vital for future conservation and biodiversity efforts. In an era where biodiversity is under threat from various environmental pressures, there is an urgent need for centralised, accessible, and actionable data. These data allow researchers to understand the genetic factors that make a species unique, including its vulnerabilities and strengths in adapting to changing environmental conditions. The information also has direct applications in agriculture and bioengineering; understanding plant genomes helps the development of more resilient crops and more efficient biofuels.


“The Global Biodiversity Portal is designed to act as a ‘super portal,’ pulling together sequencing data from biodiversity projects worldwide into a centralised, friendly interface,” said Peter Harrison, Genome Analysis Team Leader at EMBL-EBI. “This allows users to effortlessly search for all the information they need about the species they are interested in.”

“EMBL is deeply committed to understanding the intricate relationships between organisms and their environments at a molecular level,” said Josipa Bilic Zimmermann, Planetary Biology Program Manager at EMBL. “The Global Biodiversity Portal provides, in a centralised and easily accessible way, genomic information from species collected across different ecosystems on Earth. It aligns perfectly with the Planetary Biology mission, as the available information contributes to biodiversity assessment, and further genomic analysis will allow better understanding of species evolution and adaptation. Supporting projects like this is important at EMBL, as the genomic blocks of life, in all its diversity, are the basis of any further research in biology.”


Global Biodiversity

The Earth BioGenome Project represents a monumental effort to sequence, catalogue, and analyse the genomes of all eukaryotic life forms on Earth. It aims to serve as an invaluable resource for researchers across different disciplines. EMBL’s Global Biodiversity Portal will act as a comprehensive genomic platform to support the Earth BioGenome Project by making the data collected from the numerous projects that make up this wider initiative accessible all in one place.

“Data collected for the Earth BioGenome Project underpin critical scientific insights that will help researchers across the globe find solutions for some of our biggest global challenges, including climate change, disease spread across species, and conservation,” said Mark Blaxter, Programme Lead for Tree of Life Programme and Senior Group Leader at the Wellcome Sanger Institute. “Having these species data easily accessible and openly available to everyone is the fundamental core of this project and this data portal will make it possible.”


Useful features

The Global Biodiversity Portal will act as a central hub for biodiversity information by combining genomic data and metadata in a user-friendly interface that can be easily navigated and searched.


Key features of the Global Biodiversity Portal

  • Status tracking: sequencing progress can be tracked using a status tracking feature that includes information on public raw data, assemblies, and annotations for each species. The Genomes on a Tree service tracks the overall Earth BioGenome project progress, including before sampling and after sequencing have taken place.

  • Search flexibility: users will be able to search by common names as well as Latin names, aiding more accessible navigation.

  • Publications: publications that have used the genomic data collected within the portal are tracked and listed as part of the platform.

  • Related project data: users will be offered the option to visit project-specific portals for more detailed data.

  • User engagement: images and species information are provided throughout the portal, making it easy for a non-scientific audience to browse and learn more about different species.


“We are looking to continue to grow the portal by integrating holistic data including detailed locations from where the samples were collected, including climate and geographical information,” said Harrison. “We also want to incorporate data from the IUCN Red List of threatened species to provide information about the endangerment status of specific species to add further value for our users.”


Scalable data access

The portal is designed to serve both scientific and non-scientific communities, with user-friendly options to search for data related to species of interest. Its robust search functionality coupled with dynamic filtering options means that whether you’re an expert in genomics looking for specific sequencing data or a conservationist interested in habitat distribution, the portal enables a customisable search experience that brings the most relevant data to your fingertips.


The system behind the Global Biodiversity Portal is designed to convert and standardise data, allowing data harmonisation from the various sources and projects. The system updates multiple times a day, automatically scanning various databases to keep the information as current as possible. The portal is also designed with scalability in mind, both in terms of the amount of data it will handle and the number of users it needs to support as global biodiversity initiatives begin to ramp up.


“This portal represents a significant advancement for the scientific community, providing a comprehensive platform for accessing and sharing vital genomic data,” said Camila Mazzoni, Group Leader at the Leibniz Institute for Zoo and Wildlife Research Berlin and Founding Chair of the European Reference Genome Atlas (ERGA). “Our efforts at ERGA have been dedicated to mapping the genomic diversity of European species, and this new data portal will help us expand our vision on a global scale. Through this collaborative effort, we can enhance our understanding of global biodiversity, linking data from various ecosystems to support more effective and informed conservation strategies worldwide.”


Funding

This project was funded by EMBL core funding, as part of the EMBL Planetary Biology Transversal Theme.


Planetary biology at EMBL EMBL’s Planetary Biology theme delves into the molecular intricacies of life within its natural context with aims to dissect ecosystems at a mechanistic level, offering insights into the ever-evolving tapestry of biodiversity and devising ecological solutions to alleviate the strains on our planet. EMBL researchers are set to explore the complex dependencies and adaptations of different organisms, both as individuals and within communities, across various scales. Find out more about EMBL’s Molecules to Ecosystems Programme and planetary biology research across EMBL.


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