ELIXIR

Last updated

ELIXIR
Mission statement We enable scientists to access and analyse life science data
Location
  • Austria (Observer)
  • Belgium
  • Czech Republic
  • Cyprus (Observer)
  • Denmark
  • Estonia
  • Finland
  • France
  • Germany
  • Greece
  • Hungary
  • Israel
  • Ireland
  • Italy
  • Luxembourg
  • The Netherlands
  • Norway
  • Portugal
  • Romania (Observer)
  • Slovenia
  • Spain
  • Sweden
  • Switzerland
  • United Kingdom
Website www.elixir-europe.org

ELIXIR (the European life-sciences infrastructure for biological information) is an initiative that allows life science laboratories across Europe to share and store their research data as part of an organised network. Its goal is to bring together Europe's research organisations and data centres to help coordinate the collection, quality control and storage of large amounts of biological data produced by life science experiments. ELIXIR aims to ensure that biological data is integrated into a federated system easily accessible by the scientific community. [1]

Contents

Mission

Participants of a hackathon organized by ELIXIR in Terrassa Biohackathon europe group photo.jpg
Participants of a hackathon organized by ELIXIR in Terrassa

ELIXIR's mission is to build a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine and the environment, the bio-industries and society. [3]

The results from biological experiments produce vast amounts of results that are stored as data using computer software. European countries have invested heavily in research that produces, analyses and stores biological information. [4] However, the collection, storage, archiving and integration of these large amounts of data presents a problem that cannot be tackled by one country alone. ELIXIR represents the joining of independent bioscience facilities to create an integrated network that addresses the complex problem of biological data storage and management. By providing a sustainable and distributed structure for handling data and data retrieval tools, ELIXIR hopes to secure Europe-wide investment in bioinformatics, providing the stability to conduct research in all areas of life science, both in academia and industry. [1]

Organisation and structure

ELIXIR is an inter-governmental organisation which brings together existing bioinformatics resources. It is coordinated by the ELIXIR Hub, based alongside the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) on the Wellcome Trust Genome Campus in Hinxton, Cambridge.

The members of the ELIXIR consortium are European countries, represented by their governments and ministries; the scientific community in each member country develops their national Node, which operates the services and resources that are part of ELIXIR. Each ELIXIR Node is itself a network of national life science organisations, coordinated by a lead institute.

European Molecular Biology Laboratory is an intergovernmental organisation so it is the only Node that is not associated with a country.

ELIXIR focuses efforts around five central areas of activity, referred to as Platforms. These cover Data, Tools, Compute, Interoperability and Training. Work in these areas is intended to improve access to open data resources and tools by improving connectivity, discoverability and access to computational power, as well as developing training for users and service providers to meet these aims.

ELIXIR supports users addressing the Grand Challenges in life science research across diverse domains. ELIXIR supports a range of self-selected Communities, which focus on high-level topics such as ‘Human Data’ and ‘Plant Sciences’ to more specific and focused disciplines such as ‘Metabolomics’ and ‘Intrinsically Disordered Proteins’, as well as a community dedicated to the ‘Galaxy’ resource. These communities are in place to develop bioinformatic and data standards, services and training that are required to facilitate that community to reach their scientific goals.

Participants

As of September 2023 the following countries and EMBL-EBI have signed the ELIXIR Consortium Agreement (ECA) in order to become a member of ELIXIR: Belgium, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Slovenia, Spain, Sweden, Switzerland, and the United Kingdom.

Austria, Cyprus and Romania are Observer countries, working towards ratifying the ECA in the near future.

Countries that have signed the ECA are allocated representation on the ELIXIR Board.

The preparatory phase of ELIXIR was coordinated by Professor Dame Janet Thornton of EMBL-EBI.

The Founding Director of ELIXIR, Dr Niklas Blomberg, took up his position in the new ELIXIR Hub in Cambridge in May 2013. [5] He left ELIXIR in December 2023 and Prof Tim Hubbard has been appointed the new Director as of March 2024 [6] .

Funding

By the end of 2012 ELIXIR completed its five-year preparatory phase funded by the EU's Seventh Framework Programme [7] as part of the European Strategy Forum on Research Infrastructures (ESFRI) process.

In 2015 ELIXIR was awarded €19 Million HORIZON 2020 funding to run the EXCELERATE project, this was followed by the CONVERGE project in 2020. [8] [9] Both projects enabled ELIXIR to coordinate and extend national and international data resources. [10] ELIXIR has also set up collaborations to apply for other large scale funding for other EU projects, in which it is also involved in an organisational capacity, for example for the CORBEL, FAIRplus, EOSC-Life, B1MG, GDI and BY-COVID projects.

Each member state jointly contributes towards the funding of the ELIXIR Hub in proportion to their GDP. Some countries have allocated new funds to contribute towards their ELIXIR Node. The services and activities of the ELIXIR Nodes will continue to be funded by national agencies. Collectively, ELIXIR members will apply for additional external funding.

In 2024, ELIXIR commences its fourth five-year scientific programme [11] .

Related Research Articles

<span class="mw-page-title-main">European Molecular Biology Laboratory</span> Molecular biology research institution

The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 28 member states, one prospect state, and one associate member state. EMBL was created in 1974 and is funded by public research money from its member states. Research at EMBL is conducted by approximately 110 independent research and service groups and teams covering the spectrum of molecular biology and bioinformatics. The list of Groups and Teams at EMBL can be found at www.embl.org. The Laboratory operates from six sites: the main laboratory in Heidelberg, and sites in Hinxton, Grenoble (France), Hamburg (Germany), Rome (Italy) and Barcelona (Spain). EMBL groups and laboratories perform basic research in molecular biology and molecular medicine as well as train scientists, students, and visitors. The organization aids in the development of services, new instruments and methods, and technology in its member states. Israel is the only full member state located outside Europe.

<span class="mw-page-title-main">UniProt</span> Database of protein sequences and functional information

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States.

The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.

The myGrid consortium produces and uses a suite of tools design to “help e-Scientists get on with science and get on with scientists”. The tools support the creation of e-laboratories and have been used in domains as diverse as systems biology, social science, music, astronomy, multimedia and chemistry.

The EB-eye, also known as EBI Search, is a search engine that provides uniform access to the biological data resources hosted at the European Bioinformatics Institute (EBI).

The European Molecular Biology network (EMBnet) is an international scientific network and interest group that aims to enhance bioinformatics services by bringing together bioinformatics expertises and capacities. On 2011 EMBnet has 37 nodes spread over 32 countries. The nodes include bioinformatics related university departments, research institutes and national service providers.

<span class="mw-page-title-main">Wellcome Genome Campus</span> Scientific research campus in Hinxton, Cambridgeshire, England

The Wellcome Genome Campus is a scientific research campus built in the grounds of Hinxton Hall, Hinxton in Cambridgeshire, England.

<span class="mw-page-title-main">Janet Thornton</span> British bioinformatician and academic

Dame Janet Maureen Thornton, is a senior scientist and director emeritus at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function. She served as director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR.

<span class="mw-page-title-main">ChEMBL</span> Chemical database of bioactive molecules also having drug-like properties

ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug inducing properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory (EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK.

<span class="mw-page-title-main">European Nucleotide Archive</span> Online database from the EBI on Nucleotides

The European Nucleotide Archive (ENA) is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores complementary information such as experimental procedures, details of sequence assembly and other metadata related to sequencing projects. The archive is composed of three main databases: the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA is produced and maintained by the European Bioinformatics Institute and is a member of the International Nucleotide Sequence Database Collaboration (INSDC) along with the DNA Data Bank of Japan and GenBank.

<span class="mw-page-title-main">Terri Attwood</span> British bioinformatics researcher

Teresa K. Attwood is a professor of Bioinformatics in the Department of Computer Science and School of Biological Sciences at the University of Manchester and a visiting fellow at the European Bioinformatics Institute (EMBL-EBI). She held a Royal Society University Research Fellowship at University College London (UCL) from 1993 to 1999 and at the University of Manchester from 1999 to 2002.

<span class="mw-page-title-main">CLARIN</span>

Common Language Resources and Technology Infrastructure is a European Research Infrastructure Consortium founded in 2012. It comprises national consortia in and outside the European Union, consisting of institutes such as universities, research centres, libraries and public archives. The goal of the consortium is providing access to digital language data collections, to digital tools, and training material for researchers to work with the language resources.

<span class="mw-page-title-main">European Multidisciplinary Seafloor and water column Observatory</span> Large-scale European distributed Research Infrastructure for ocean observation

European Multidisciplinary Seafloor and water-column Observatory (EMSO) is a large-scale European distributed Research Infrastructure for ocean observation, enabling real-time interactive long term monitoring of ocean processes. EMSO allows study of the interaction between the geosphere, the biosphere, the hydrosphere, and the lithosphere; including natural hazards, climate change, and marine ecosystems. EMSO nodes have been deployed at key sites in European seas, starting from the Arctic, through the Atlantic and Mediterranean, to the Black Sea.

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure initiated by the Federal Ministry of Education and Research funding 2015-2021. The network provides bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data. From 2022, the network will be integrated into Forschungszentrum Jülich.

The Global Alliance for Genomics and Health (GA4GH) is an international consortium that is developing standards for responsibly collecting, storing, analyzing, and sharing genomic data in order to enable an "internet of genomics". GA4GH was founded in 2013.

<span class="mw-page-title-main">Manuel Corpas (scientist)</span> British bioinformatics researcher

Manuel Corpas is an Anglo-Spanish biologist and entrepreneur known primarily for his contributions to the field of Bioinformatics and Genomics. Currently Corpas is Chief Scientist of Cambridge startup Cambridge Precision Medicine, a tutor at the Institute for Continuing Education at the University of Cambridge and a lecturer at the Universidad Internacional de La Rioja. Manuel worked on the human genome from the beginning of his career, being one of the first consumers to sequence and his own genome and that of close relatives, which he published as the Corpasome. He has held positions at the Earlham Institute as Project Leader, and the Wellcome Sanger Institute, developing the DECIPHER database, a database that aids in the diagnosis of patients with rare genomic disorders.

The Ontology Lookup Service (OLS) is a repository for biomedical ontologies, part of the ELIXIR infrastructure. It is supported by the European Bioinformatics Institute (EMBL-EBI).

Protein Data Bank in Europe – Knowledge Base (PDBe-KB) is a community-driven, open-access, integrated resource whose mission is to place macromolecular structure data in their biological context and to make them accessible to the scientific community in order to support fundamental and translational research and education. It is part of the European Bioinformatics Institute (EMBL-EBI), based at the Wellcome Genome Campus, Hinxton, Cambridgeshire, England.

Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.

<span class="mw-page-title-main">Susanna-Assunta Sansone</span> British-Italian data scientist

Susanna-Assunta Sansone is a British-Italian data scientist who is professor of data readiness at the University of Oxford where she leads the data readiness group and serves as associate director of the Oxford e-Research Centre. Her research investigates techniques for improving the interoperability, reproducibility and integrity of data.

References

  1. 1 2 Crosswell, L. C.; Thornton, J. M. (2012). "ELIXIR: A distributed infrastructure for European biological data". Trends in Biotechnology. 30 (5): 241–242. doi:10.1016/j.tibtech.2012.02.002. PMID   22417641.
  2. ↑ "BioHackathon Europe". biohackathon-europe.org. Retrieved 26 November 2021.
  3. ↑ ELIXIR (2 September 2019). "ELIXIR Scientific Programme 2019-2023". F1000Research. 8 (1570): 1570. doi: 10.7490/f1000research.1117352.1 .
  4. ↑ "ELIXIR Business Case" (PDF). Archived from the original (PDF) on 23 April 2013. Retrieved 25 April 2013.
  5. ↑ "ELIXIR appoints Founding Director". ELIXIR. 5 February 2013. Retrieved 16 November 2023.
  6. ↑ "Tim Hubbard to be new ELIXIR Director". ELIXIR. 1 December 2023. Retrieved 8 January 2024.
  7. ↑ Economic and Social Research Council description of FP7. Archived 2011-09-01 at the Wayback Machine
  8. ↑ ELIXIR (11 May 2015). "ELIXIR accelerates with major Horizon 2020 funding". ELIXIR. Retrieved 30 September 2019.
  9. ↑ "ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences". CORDIS. European Commission. Retrieved 30 September 2019.
  10. ↑ ELIXIR (2 September 2019). "Successful completion of ELIXIR-EXCELERATE marks new stage in ELIXIR's development". ELIXIR. Retrieved 30 September 2019.
  11. ↑ "ELIXIR publishes 2024-28 Scientific Programme". ELIXIR. 4 December 2023. Retrieved 8 January 2024.
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