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1. The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

Author

Waterhouse, Robert M., primary, Adam-Blondon, Anne-Françoise, additional, Balech, Bachir, additional, Barta, Endre, additional, Ying Shi Chua, Physilia, additional, Di Cola, Valeria, additional, Heil, Katharina F., additional, Hughes, Graham M., additional, Jermiin, Lars S., additional, Kalaš, Matúš, additional, Lanfear, Jerry, additional, Pafilis, Evangelos, additional, Palagi, Patricia M., additional, Papageorgiou, Aristotelis C., additional, Paupério, Joana, additional, Psomopoulos, Fotis, additional, Raes, Niels, additional, Burgin, Josephine, additional, and Gabaldón, Toni, additional

Published
2024
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2. Beyond BiCIKL: Towards Building an AI-Assisted “Biodiversity Supergraph”

Author

Penev, Lyubomir, Koureas, D. (Dimitris), Groom, Quentin, Lanfear, Jerry, Agosti, Donat, Casino, Ana, Miller, Joe, Cochrane, Guy, Banki, O. (Olaf), Kõljalg, Urmas, Ruch, Patrick, Güntsch, Anton, Benito Gonzalez Lopez, J. (Jose), Mergen, Patricia, Pauperio, Joana, Kuhn, Tobias, Minadakis, Nikos, Smith, Vincent, Arvanitidis, Christos, Penev, Lyubomir, Koureas, D. (Dimitris), Groom, Quentin, Lanfear, Jerry, Agosti, Donat, Casino, Ana, Miller, Joe, Cochrane, Guy, Banki, O. (Olaf), Kõljalg, Urmas, Ruch, Patrick, Güntsch, Anton, Benito Gonzalez Lopez, J. (Jose), Mergen, Patricia, Pauperio, Joana, Kuhn, Tobias, Minadakis, Nikos, Smith, Vincent, and Arvanitidis, Christos

Abstract

BiCIKL (Biodiversity Community Integrated Knowledge Library) is a European Union (EU) Horizon 2020 project (2021–2024) building a new community of research infrastructures (RIs), researchers and other stakeholders, through improved access to interlinked, open and FAIR (Findable, Accessible, Interoperable, Reusable) biodiversity data along the biodiversity research cycle (specimens, sequences, taxon names, publications) (Penev et al. 2022). The project’s 14 partners developed or substantially improved 16 tools and services currently in process of onboarding to the European Open Science Cloud (EOSC), presented in the FAIR Data Place (FDP) of BiCIKL’s flagship product, the Biodiversity Knowledge Hub (BKH). The tools and data were used in Open Call projects, performed by research groups worldwide. A key achievement of BiCIKL is the establishment of several new bi-directional links between the participating RIs through shared and interoperable data standards and web services. The sustainability of the BiCIKL services and especially of the strong collaborative spirit developed through the project will be ensured by a membership agreement for the BKH maintenance and further development. The results of BiCIKL are diverse and tackle various aspects of the implementation of open science practices in biodiversity research. The project partners and external collaborators from the Open Call projects published more than 80 papers and conference abstracts (see the article collections in Penev et al. 2022a and Thessen et al. 2023), two policy briefs (Penev et al. 2024, Agosti et al. 2024), three Biodiversity Information Science (TDWG) symposia (2021, 2023, 2024), several videos and factsheets and other training materials, guidelines and best practice recommendations, and so on. In the special focus of BiCIKL was the extraction and liberation of data from the PDFs of several thousands of published biodiversity articles making it accessible and re-usable. The new BiCIKL community pro

Published
2024
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4. The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Cochrane, Guy, additional, Pauperio, Joana, additional, Bánki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Ruch, Patrick, additional, Hristova, Kristina, additional, Barov, Boris, additional, Madeira Scauri, Madeira, additional, Montinaro, Sara, additional, Vaira, Lucia, additional, Fiore, Nicola, additional, Bamford, Elizabeth, additional, and Arvanitidis, Christos, additional

Published
2023
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5. The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity

Author

Waterhouse, Robert M., primary, Adam-Blondon, Anne-Françoise, additional, Balech, Bachir, additional, Barta, Endre, additional, Heil, Katharina F., additional, Hughes, Graham M., additional, Jermiin, Lars S., additional, Kalaš, Matúš, additional, Lanfear, Jerry, additional, Pafilis, Evangelos, additional, Papageorgiou, Aristotelis C., additional, Psomopoulos, Fotis, additional, Raes, Niels, additional, Burgin, Josephine, additional, and Gabaldón, Toni, additional

Published
2023
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6. Deliverable D8.3 Web interface for ELIXIR Contextual Data ClearingHouse

Author

Abarenkov, Kessy, Zirk, Allan, Cochrane, Guy, Balavenkataraman Kadhirvelu, Vishnukumar, Pauperio, Joana, Bánki, Olaf, Lanfear, Jerry, Ivanov, Filipp, Piirmann, Timo, Pöhönen, Raivo, and Kõljalg, Urmas

Subjects
BiCIKL
Abstract

This deliverable report includes description of the work steps towards building a web interface for the reporting of errors and gaps in sequenced material source annotations as part of the Task 8.3 of BiCIKL. Beta version of the web interface has been published and is available for the registered users of PlutoF platform.

Published
2023
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7. The Biodiversity Knowledge Hub (BKH): A Crosspoint and Knowledge Broker for FAIR and Linked Biodiversity Data.

Author

Penev, Lyubomir, Koureas, Dimitrios, Groom, Quentin, Lanfear, Jerry, Agosti, Donat, Casino, Ana, Miller, Joe, Cochrane, Guy, Pauperio, Joana, Bánki, Olaf, Addink, Wouter, Kõljalg, Urmas, Ruch, Patrick, Hristova, Kristina, Barov, Boris, Scauri, Madeira Madeira, Montinaro, Sara, Vaira, Lucia, Fiore, Nicola, and Bamford, Elizabeth

Subjects
BIODIVERSITY research, TAXONOMY, INTERNETWORKING, INFRASTRUCTURE (Economics), DATA integration
Abstract

The Biodiversity Knowledge Hub (BKH) is a web platform acting as an integration point and broker of an open, FAIR (Findable, Accessible, Interoperable, Reusable) and interlinked corpora of biodiversity data, services and knowledge. It serves the entire biodiversity research cycle, from specimens and observations to sequences, taxon names and finally to scientific publications. The strategic aim of the BKH is to support a functional and integrated biodiversity knowledge graph and an emerging new community of users. The BKH is aimed at biodiversity researchers in the widest sense, research infrastructures and publishers (Fig. 1). The BKH is the key product of the EU-funded Biodiversity Community Integrated Knowledge Library (BiCIKL) project (Penev et al. 2022). The four goals of BiCIKL and the BKH are: 1. Improved access to open and FAIR biodiversity data; 2. Establishing of bi-directional data linkages between infrastructures; 3. Development of new methods and workflows for semantic publishing, harvesting, liberating, linking, accessing and re-using of data in literature (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables); 4. Testing and implementation of services through use cases and open call projects for researchers outside the project. The BKH consists of several modules, such as the Home page that presents the main user groups and the benefits that the BKH provides to them. It has guidelines and protocols, such as various documents on the policies, functions, and recommendations for the users. And it has relevant projects, that use linked FAIR biodiversity data. In the core of the BKH is the FAIR Data Place (FDP), which presents novel services and tools developed over the course of BiCIKL. In the future, the FDP will also accept services for linked data provided by new contributors. The FDP consists of three sub-modules: • Infrastructures and organisations: Lists the contributing organisations and research infrastructures with short descriptions and links to their data, tools and services. Research infrastructures are sorted by the main type of biodiversity data they aggregate and serve: specimens, sequences, taxon names and literature. • Linked data services: A catalogue of novel services that deliver FAIR data linked between the participating research infrastructures. Examples of such services are: ChecklistBank, LifeBlock, OpenBiodiv, TreatmentBank, SIBiLS "BiodiversityPMC", eBioDiv, SynoSpecies, PlutoF Curation Tool and others. • Become a contributor application form: A formal questionnaire which serves as a basis to check the suitability of an organisation or research infrastructure to join the BKH. Part of the application form is a FAIR data checklist. The BKH serves as a navigation system in a universe of interconnected biodiversity research infrastructures and is open to new contributors and collaborators in accessing open data and knowledge by anybody, anywhere, at any time. [ABSTRACT FROM AUTHOR]

Published
2023
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8. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Author

Waterhouse, Robert M., Adam-Blondon, Anne-Françoise, Agosti, Donat, Baldrian, Petr, Balech, Bachir, Corre, Erwan, Davey, Robert P., Lantz, Henrik, Pesole, Graziano, Quast, Christian, Glöckner, Frank Oliver, Raes, Niels, Sandionigi, Anna, Santamaria, Monica, Addink, Wouter, Vohradsky, Jiri, Nunes-Jorge, Amandine, Willassen, Nils Peder, and Lanfear, Jerry

Subjects
General Pharmacology, Toxicology and Pharmaceutics, General Immunology and Microbiology, General Biochemistry, Genetics and Molecular Biology, General Medicine
Abstract

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.

Published
2022

9. Enabling Community Curation of Biological Source Annotations of Molecular Data Through PlutoF and the ELIXIR Contextual Data Clearinghouse

Author

Balavenkataraman Kadhirvelu, Vishnukumar, primary, Abarenkov, Kessy, additional, Zirk, Allan, additional, Paupério, Joana, additional, Cochrane, Guy, additional, Jayathilaka, Suran, additional, Bánki, Olaf, additional, Lanfear, Jerry, additional, Ivanov, Filipp, additional, Piirmann, Timo, additional, Pöhönen, Raivo, additional, and Kõljalg, Urmas, additional

Published
2022
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11. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Author

Waterhouse, Robert M., primary, Adam-Blondon, Anne-Françoise, additional, Agosti, Donat, additional, Baldrian, Petr, additional, Balech, Bachir, additional, Corre, Erwan, additional, Davey, Robert P., additional, Lantz, Henrik, additional, Pesole, Graziano, additional, Quast, Christian, additional, Glöckner, Frank Oliver, additional, Raes, Niels, additional, Sandionigi, Anna, additional, Santamaria, Monica, additional, Addink, Wouter, additional, Vohradsky, Jiri, additional, Nunes-Jorge, Amandine, additional, Willassen, Nils Peder, additional, and Lanfear, Jerry, additional

Published
2022
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13. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Author

Waterhouse, Robert M, Adam-Blondon, Anne-Françoise, Agosti, Donat, Baldrian, Petr, Balech, Bachir, Corre, Erwan, Davey, Robert P, Lantz, Henrik, Pesole, Graziano, Quast, Christian, Glöckner, Frank Oliver, Raes, Niels, Sandionigi, Anna, Santamaria, Monica, Addink, Wouter, Vohradsky, Jiri, Nunes-Jorge, Amandine, Willassen, Nils Peder, Lanfear, Jerry, Waterhouse, Robert M, Adam-Blondon, Anne-Françoise, Agosti, Donat, Baldrian, Petr, Balech, Bachir, Corre, Erwan, Davey, Robert P, Lantz, Henrik, Pesole, Graziano, Quast, Christian, Glöckner, Frank Oliver, Raes, Niels, Sandionigi, Anna, Santamaria, Monica, Addink, Wouter, Vohradsky, Jiri, Nunes-Jorge, Amandine, Willassen, Nils Peder, and Lanfear, Jerry

Abstract

Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to delive

Published
2022

14. Web interface for ELIXIR Contextual Data ClearingHouse.

Author

Abarenkov, Kessy, Zirk, Allan, Cochrane, Guy, Kadhirvelu, Vishnukumar, Jayathilaka, Suran, Paupério, Joana, Banki, Olaf, Lanfear, Jerry, Ivanov, Filipp, Piirmann, Timo, Pöhönen, Raivo, and Kõljalg, Urmas

Subjects
USER interfaces, COMPUTER software development, MACHINE learning, ARTIFICIAL intelligence, DATA analysis
Published
2023
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15. Biodiversity Community Integrated Knowledge Library (BiCIKL)

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, Demirova, Iliyana, additional, and Hristova, Kristina, additional

Published
2022
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16. Figure 9 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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17. Figure 4 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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18. Figure 8 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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19. Figure 1 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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20. Supplementary material 1 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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21. Figure 7 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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22. Figure 3 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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23. Supplementary material 2 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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24. Supplementary material 3 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Demirova I, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, Demirova, Iliyana, additional, and Hristova, Kristina, additional

Published
2022
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25. Figure 6 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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26. Figure 2 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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27. Figure 5 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Hobern D, Banki O, Addink W, Kõljalg U, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J, Ruch P, Martin CS, Barov B, Hristova K (2022) Biodiversity Community Integrated Knowledge Library (BiCIKL). Research Ideas and Outcomes 8: e81136. https://doi.org/10.3897/rio.8.e81136

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, Benito Gonzalez Lopez, Jose, additional, Ruch, Patrick, additional, Martin, Corinne, additional, Barov, Boris, additional, and Hristova, Kristina, additional

Published
2022
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28. Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective

Author

Penev, Lyubomir, Koureas, Dimitrios, Groom, Quentin, Lanfear, Jerry, Agosti, Donat, Casino, Ana, Miller, Joe, Arvanitidis, Christos, Cochrane, Guy, Barov, Boris, Hobern, Donald, Banki, Olaf, Addink, Wouter, Kõljalg, Urmas, Ruch, Patrick, Copas, Kyle, Mergen, Patricia, Güntsch, Anton, Benichou, Laurence, and Benito Gonzalez Lopez, Jose

Subjects
Data linking, Perspective (graphical), literature, Biodiversity, Environmental ethics, General Medicine, research infrastructures, taxon names, specimens, sequences, Sociology, FAIR biodiversity data, data linking
Abstract

The Horizon 2020 project Biodiversity Community Integrated Knowledge Library (BiCIKL) (started 1st of May 2021, duration 3 years) will build a new European community of key research infrastructures, researchers, citizen scientists and other stakeholders in biodiversity and life sciences. Together, the BiCIKL 14 partners will solidify open science practices by providing access to data, tools and services at each stage of, and along the entire biodiversity research and data life cycle (specimens, sequences, taxon names, analytics, publications, biodiversity knowledge graph) (Fig. 1, see also the BiCIKL kick-off presentation through Suppl. material 1), in compliance with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. The existing services provided by the participating infrastructures will expand through development and adoption of shared, common or interoperable domain standards, resulting in liberated and enhanced flows of data and knowledge across these domains. BiCIKL puts a special focus on the biodiversity literature. Over the span of the project, BiCIKL will develop new methods and workflows for semantic publishing and integrated access to harvesting, liberating, linking, and re-using sub-article-level data extracted from literature (i.e., specimens, material citations, sequences, taxonomic names, taxonomic treatments, figures, tables). Data linkages may be realised with different technologies (e.g., data warehousing, linking between FAIR Data Objects, Linked Open Data) and can be bi-lateral (between two data infrastructures) or multi-lateral (among multiple data infrastructures). The main challenge of BiCIKL is to design, develop and implement a FAIR Data Place (FDP), a central tool for search, discovery and management of interlinked FAIR data across different domains. The key final output of BiCIKL will the future Biodiversity Knowledge Hub (BKH), a one-stop portal, providing access to the BiCIKL services, tools and workflows, beyond the lifetime of the project.

Published
2021

29. Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR

Author

Waterhouse, Robert M., primary, Adam-Blondon, Anne-Françoise, additional, Agosti, Donat, additional, Baldrian, Petr, additional, Balech, Bachir, additional, Corre, Erwan, additional, Davey, Robert P., additional, Lantz, Henrik, additional, Pesole, Graziano, additional, Quast, Christian, additional, Glöckner, Frank Oliver, additional, Raes, Niels, additional, Sandionigi, Anna, additional, Santamaria, Monica, additional, Addink, Wouter, additional, Vohradsky, Jiri, additional, Nunes-Jorge, Amandine, additional, Willassen, Nils Peder, additional, and Lanfear, Jerry, additional

Published
2021
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30. Supplementary material 1 from: Penev L, Koureas D, Groom Q, Lanfear J, Agosti D, Casino A, Miller J, Arvanitidis C, Cochrane G, Barov B, Hobern D, Banki O, Addink W, Kõljalg U, Ruch P, Copas K, Mergen P, Güntsch A, Benichou L, Benito Gonzalez Lopez J (2021) Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective. Biodiversity Information Science and Standards 5: e74233. https://doi.org/10.3897/biss.5.74233

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Barov, Boris, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Ruch, Patrick, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, and Benito Gonzalez Lopez, Jose, additional

Published
2021
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31. Towards Interlinked FAIR Biodiversity Knowledge: The BiCIKL perspective

Author

Penev, Lyubomir, primary, Koureas, Dimitrios, additional, Groom, Quentin, additional, Lanfear, Jerry, additional, Agosti, Donat, additional, Casino, Ana, additional, Miller, Joe, additional, Arvanitidis, Christos, additional, Cochrane, Guy, additional, Barov, Boris, additional, Hobern, Donald, additional, Banki, Olaf, additional, Addink, Wouter, additional, Kõljalg, Urmas, additional, Ruch, Patrick, additional, Copas, Kyle, additional, Mergen, Patricia, additional, Güntsch, Anton, additional, Benichou, Laurence, additional, and Benito Gonzalez Lopez, Jose, additional

Published
2021
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34. The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

Author

Drysdale, Rachel, Cook, Charles E, Petryszak, Robert, Baillie-Gerritsen, Vivienne, Barlow, Mary, Gasteiger, Elisabeth, Gruhl, Franziska, Haas, Jürgen, Lanfear, Jerry, Lopez, Rodrigo, Redaschi, Nicole, Stockinger, Heinz, Teixeira, Daniel, Venkatesan, Aravind, Bateman, Alex, Bridge, Alan, Cochrane, Guy, Finn, Rob, Glöckner, Frank Oliver, Hanauer, Marc, Keane, Thomas, Leach, Andrew, Licata, Luana, Oksvold, Per, Orchard, Sandra, Orengo, Christine, Parkinson, Helen, Persson, Bengt, Porras, Pablo, Rambla, Jordi, Rath, Ana, Rodwell, Charlotte, Sarkans, Ugis, Schomburg, Dietmar, Sillitoe, Ian, Spalding, Dylan, Uhlén, Mathias, Velankar, Sameer, Vizcaíno, Juan Antonio, von Feilitzen, Kalle, von Mering, Christian, Yates, Andrew, Blomberg, Niklas, Durinx, Christine, McEntyre, Johanna, Drysdale, Rachel, Cook, Charles E, Petryszak, Robert, Baillie-Gerritsen, Vivienne, Barlow, Mary, Gasteiger, Elisabeth, Gruhl, Franziska, Haas, Jürgen, Lanfear, Jerry, Lopez, Rodrigo, Redaschi, Nicole, Stockinger, Heinz, Teixeira, Daniel, Venkatesan, Aravind, Bateman, Alex, Bridge, Alan, Cochrane, Guy, Finn, Rob, Glöckner, Frank Oliver, Hanauer, Marc, Keane, Thomas, Leach, Andrew, Licata, Luana, Oksvold, Per, Orchard, Sandra, Orengo, Christine, Parkinson, Helen, Persson, Bengt, Porras, Pablo, Rambla, Jordi, Rath, Ana, Rodwell, Charlotte, Sarkans, Ugis, Schomburg, Dietmar, Sillitoe, Ian, Spalding, Dylan, Uhlén, Mathias, Velankar, Sameer, Vizcaíno, Juan Antonio, von Feilitzen, Kalle, von Mering, Christian, Yates, Andrew, Blomberg, Niklas, Durinx, Christine, and McEntyre, Johanna

Published
2020
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36. Going Molecular: Sequence-based spatiotemporal biodiversity evidence in GBIF

Author

Schigel, Dmitry, Jeppesen, Thomas, Finn, Robert, Cochrane, Guy, Kõljalg, Urmas, Quast, Christian, Lanfear, Jerry, Orrell, Thomas, Hobern, Donald, and Miller, Joseph

Abstract

The Global Biodiversity Information Facility (GBIF) was established by governments in 2001, largely through the initiative and leadership of the natural history collections community, following the 1999 recommendation by a working group under the Megascience Forum (predecessor of the Global Science Forum) of the Organization for Economic Cooperation and Development (OECD). Over 20 years, GBIF has helped develop standards and convened a global community of data-publishing institutions, aggregrating over one billion specimen occurrence records freely and openly available for use in research and policy making. These GBIF mediated data range from vouchered museum specimens to observation records generated by humans and machines. New data are being generated from integrated remote sensing, ecological sampling, and molecular sequencing that have strong geospatial components but lack traditional vouchers. GBIF is working with partners to develop best practices of bringing this data into the GBIF architecture. Following discussions during the second Global Biodiversity Information Conference in 2018, GBIF and the European Bioinformatics Institute (EMBL-EBI), supported by ELIXIR, have extended collaboration to share species occurrence records known only from their genetic material. When these data providers contribute data coordinates along with the sequences to the European Nucleotide Archive (ENA), the records will appear on GBIF maps and in spatial searches. This collaboration enables significant new molecular data streams to become discoverable through GBIF.org: by mid-March 2019, over 7.8m individual occurrence records via the ENA, and over 13.2m records as standardized Darwin Core sampling-event datasets via MGnify, a resource that provides taxonomic and functional annotations on sequences derived from environmental sequencing projects. Sequence-based occurrence records published by ENA and MGnify boost representation of microbial diversity which was underrepresented at GBIF. The ELIXIR-ENA-MGnify-GBIF partnership is working on further refinement of the dynamic data linkages, frequency of updates and other improvements. The API-based tool that connects GBIF data infrastructures is open to new data contributors and for indexes of molecular occurrences. Indexing of these data streams is dependent on the presence of a name (any rank) with the sequence. Under the current Codes of nomenclature, animals, fungi, plants, and algae cannot be described based on exclusively sequence data. Yet, a significant volume of biodiversity data has only been represented by DNA sequences. Barcoding and sequence clustering procedures vary among taxa and research communities, but clusters can be related to a taxon with a Latin name. Many DNA similarity clusters do not contain a sequence from a formally described taxon; however these sequence clusters provide provisional molecular names for nomenclatural communication. In the best cases, curated libraries of reference sequences, their metadata, clusters, alignments, and links to individuals and physical material become de facto naming conventions for certain taxonomic groups, and co-exist with Latin names. Integration of molecular names into the taxonomic backbone of GBIF started with Fungi and UNITE, a data management and identification environment for fungal ITS barcodes with 87,000+ fungal species hypotheses demarcating 800,000+ sequence specimens as of March 2019. Checklist publication of all names in UNITE through GBIF.org including Linnaean names and stable, DOI-trackable molecular sequence based 'species hypotheses', enables indexing of fungal metabarcoding data worldwide, such as BIOWIDE. As names are currently essential to indexing the world's occurrence data, GBIF will develop similar linkages with names in the Barcode of Life data system (BOLD) and in SILVA - a resource for high-quality ribosomal RNA sequence data and taxonomy, and welcomes other reference systems to this development. Expanding the molecular data streams (Fig. 1) allows GBIF to address spatial, temporal and taxonomic gaps and biases, and to support large-scale data-intensive research openly and worldwide.

Published
2019

37. Mainstreaming Molecular Biodiversity: A call for a unified and interoperable framework

Author

Buttigieg, Pier Luigi, Lanfear, Jerry, Glöckner, Frank Oliver, Macklin, James, Buttigieg, Pier Luigi, Lanfear, Jerry, Glöckner, Frank Oliver, and Macklin, James

Abstract

Over the past 20 years, immense progress has been made in enhancing the effectiveness, affordability, and deployability of molecular methods for biodiversity assessment and monitoring. From the micro- to macroscopic scale, methods such as amplicon sequencing of phylogenetic marker genes, metagenomics, and metatranscriptomics have greatly impacted biology and ecology, and are steadily being integrated into national and international biodiversity policy. Over the next decade, technologies such as miniaturised and autonomous DNA sequencing platforms will amplify this momentum, ushering in an unprecedented volume of deeply minable biodiversity information. While production-grade resources exist to standardise, archive, and exchange raw molecular data (e.g. the resources of the International Nucleotide Sequence Database Collaboration (INSDC) for DNA and RNA sequences), there are still no equivalent frameworks for biodiversity information derived from molecular methods. Research infrastructures in both the biodiversity and molecular biology domains must fill this gap with great urgency to channel molecular advances into efforts to understand and sustain Earth's imperilled biosphere. This session seeks to accelerate the implementation of global standards to link molecular biodiversity data to taxonomy-based systems. Only with these in place can we realise a robust, distributed, yet fully interoperating, network of infrastructures, projects, and researchers addressing molecular biodiversity. This introductory series of flash talks will present the rationale and goals of the session, alongside a joint vision from representatives of several convening stakeholders. A contribution from ELIXIR, an intergovernmental organisation of distributed infrastructures for biological data, will demonstrate the high readiness of biological data resources such as the European Nucleotide Archive (ENA) to mobilise molecular data along new standards. An intervention from the SILVA rRNA database

Published
2019

38. Building a strategy towards an Omic Biodiversity Observation Network (Omic BON)

Author

Buttigieg, Pier, Appeltans, W., Canonico, Gabrielle, Chavez, Francisco P., Deck, John, Glöckner, Frank Oliver, Goodwin, Kelly D., Hunter, Margaret, Kotoulas, Georgios, Janssen, Felix, Lanfear, Jerry, Meyer, Christopher P., Muller-Karger, Frank, Obst, Matthias, Pitz, Kathleen J., Provoost, Pieter, Thompson, Luke R., Walls, Ramona, Davies, Neil, Buttigieg, Pier, Appeltans, W., Canonico, Gabrielle, Chavez, Francisco P., Deck, John, Glöckner, Frank Oliver, Goodwin, Kelly D., Hunter, Margaret, Kotoulas, Georgios, Janssen, Felix, Lanfear, Jerry, Meyer, Christopher P., Muller-Karger, Frank, Obst, Matthias, Pitz, Kathleen J., Provoost, Pieter, Thompson, Luke R., Walls, Ramona, and Davies, Neil

Published
2019

40. D14.2 POPD - Requirement No. 4

Author

Khalem, Pascal, Lanfear, Jerry, and Becker, Regina

Abstract

This deliverable describes the ELIXIR risk management strategy with respect to the General DataProtection Regulation (GDPR)1, which came into force on 25 May 2018.The strategy describes the essential procedures and practices within ELIXIR concerning GDPRcompliance, performing risk assessment and mitigation.

Published
2018
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41. ELIXIR-EXCELERATE D13.3: Fast-track ELIXIR implementation and drive early user exploitation across the life sciences

Author

Martin, Corrine, Smith, Andrew, Blomberg, Niklas, Velek, Premysl, Balzano, Melissa, Berman, Maia, Cook, Martin, Coppens, Frederik, Drysdale, Rachel, Durinx, Christine, Hancock, John, Harrow, Jennifer, Lanfear, Jerry, Lauer, Katharina, Palagi, Patricia, Pommier, Cyril, Repo, Susanna, Sansone, Susanna, Sarntivijai, Sirarat, Saunders, Gary, Tedds, Jonathan, and van Gelder, Celia

Subjects
International, Strategy, bioinformatics, EXCELERATE, infrastructure, ELIXIR
Abstract

ELIXIR’s International Strategy describes current activities of international relevance, and planned implementation actions to reinforce ELIXIR’s global significance and impact. An update is released on an annual basis. In the context of this document, the term ‘International’ means ‘beyond Europe’, with ‘Europe’ defined as the countries of the European Research Area1 (ERA). The Strategy is articulated around four main objectives: (1) scale-up the international user base of ELIXIR’s Services, (2) improve bioinformatics services and promote global standards, (3) expand Membership in ELIXIR beyond Europe, and (4) ensure that ELIXIR is recognised as an infrastructure of global relevance, and a partner of choice by intergovernmental organisations. The international audience of the Strategy encompasses users of bioinformatics services, national-level bioinformatics infrastructures, and government officials in Ministries. Also targeted by this Strategy are international bioinformatics-related initiatives􏰀 and organisations, and intergovernmental organisations. Closer to home, the Strategy aims to raise awareness of ELIXIR’s global significance within Member countries, and guide efforts to ensure coherent implementation actions in support of the objectives of the Strategy. The strategy will be implemented through a concrete set of Actions, described in Annex I, each relating to one of the four specific Objectives.

Published
2018
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46. Identification and characterisation of the angiotensin converting enzyme-3 (ACE3) gene: a novel mammalian homologue of ACE

Author

Phelan Anne, Lanfear Jerry, Revett Timothy J, Elliot Joann L, Rella Monika, Jackson Richard M, Turner Anthony J, and Hooper Nigel M

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Mammalian angiotensin converting enzyme (ACE) plays a key role in blood pressure regulation. Although multiple ACE-like proteins exist in non-mammalian organisms, to date only one other ACE homologue, ACE2, has been identified in mammals. Results Here we report the identification and characterisation of the gene encoding a third homologue of ACE, termed ACE3, in several mammalian genomes. The ACE3 gene is located on the same chromosome downstream of the ACE gene. Multiple sequence alignment and molecular modelling have been employed to characterise the predicted ACE3 protein. In mouse, rat, cow and dog, the predicted protein has mutations in some of the critical residues involved in catalysis, including the catalytic Glu in the HEXXH zinc binding motif which is Gln, and ESTs or reverse-transcription PCR indicate that the gene is expressed. In humans, the predicted ACE3 protein has an intact HEXXH motif, but there are other deletions and insertions in the gene and no ESTs have been identified. Conclusion In the genomes of several mammalian species there is a gene that encodes a novel, single domain ACE-like protein, ACE3. In mouse, rat, cow and dog ACE3, the catalytic Glu is replaced by Gln in the putative zinc binding motif, indicating that in these species ACE3 would lack catalytic activity as a zinc metalloprotease. In humans, no evidence was found that the ACE3 gene is expressed and the presence of deletions and insertions in the sequence indicate that ACE3 is a pseudogene.

Published
2007
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47. Erratum to: Making sense of big data in health research: towards an EU action plan

Author

Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, and Zanetti, Gianluigi

Subjects
Journal Article
Published
2016

48. Correction: Making sense of big data in health research: towards an EU action plan (vol 8, pg 71, 2016)

Author

Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Muller, Werner, Nickel, Dothe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, and Zanetti, Gianluigi

Subjects
Klinisk medicin, Clinical Medicine
Abstract

n/a

Published
2016

49. Making sense of big data in health research: Towards an EU action plan

Author

Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Mueller, Werner, Nickel, Dorthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, Zanetti, Gianluigi, Auffray, Charles, Balling, Rudi, Barroso, Ines, Bencze, Laszlo, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Glynne Gut, Ivo, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Angel, Rod Hose, D., Houwing-Duistermaat, Jeanine, Hubbard, Tim, Helen Janacek, Sophie, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Mueller, Werner, Nickel, Dorthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, Redon i Mas, Josep, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A. I., van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Antonio Vizcaino, Juan, Peter Mary Wubbe, John, and Zanetti, Gianluigi

Abstract

Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with automation and miniaturization has triggered an explosion in data production that will soon reach exabyte proportions. How are we going to deal with this exponential increase in data production? The potential of "big data" for improving health is enormous but, at the same time, we face a wide range of challenges to overcome urgently. Europe is very proud of its cultural diversity; however, exploitation of the data made available through advances in genomic medicine, imaging, and a wide range of mobile health applications or connected devices is hampered by numerous historical, technical, legal, and political barriers. European health systems and databases are diverse and fragmented. There is a lack of harmonization of data formats, processing, analysis, and data transfer, which leads to incompatibilities and lost opportunities. Legal frameworks for data sharing are evolving. Clinicians, researchers, and citizens need improved methods, tools, and training to generate, analyze, and query data effectively. Addressing these barriers will contribute to creating the European Single Market for health, which will improve health arid healthcare for all Europearis., Funding Agencies|European Union [115568, 603160, 282510, 664691, 115749, 305033, 305397, 288028, 242189, 211601]; European Molecular Biology Laboratory; Wellcome Trust [WT098051]; [115372]; [257082]; [291814]; [291728]; [321567]; [262055]; [115446]; [602552]; [644753]; [634143]; [261357]; [305280]; [115525]; [2011 23 02]; [270089]; [278433]; [602525]; [201418]; [242135]; [260558]; [223411]; [305626]; [115621]; [611388]; [306000]; [354457]; [305564]; [115010]; [269978]

Published
2016
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50. Erratum to: Making sense of big data in health research: towards an EU action plan

Author

Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, Zanetti, Gianluigi, Biostatistiek Onderzoek, Circulatory Health, JC onderzoeksprogramma Infectieziekten, JC onderzoeksprogramma Methodologie, Child Health, Auffray, Charles, Balling, Rudi, Barroso, Inês, Bencze, László, Benson, Mikael, Bergeron, Jay, Bernal-Delgado, Enrique, Blomberg, Niklas, Bock, Christoph, Conesa, Ana, Del Signore, Susanna, Delogne, Christophe, Devilee, Peter, Di Meglio, Alberto, Eijkemans, Marinus, Flicek, Paul, Graf, Norbert, Grimm, Vera, Guchelaar, Henk-Jan, Guo, Yi-Ke, Gut, Ivo Glynne, Hanbury, Allan, Hanif, Shahid, Hilgers, Ralf-Dieter, Honrado, Ángel, Hose, D Rod, Houwing-Duistermaat, Jeanine, Hubbard, Tim, Janacek, Sophie Helen, Karanikas, Haralampos, Kievits, Tim, Kohler, Manfred, Kremer, Andreas, Lanfear, Jerry, Lengauer, Thomas, Maes, Edith, Meert, Theo, Müller, Werner, Nickel, Dörthe, Oledzki, Peter, Pedersen, Bertrand, Petkovic, Milan, Pliakos, Konstantinos, Rattray, Magnus, I Màs, Josep Redón, Schneider, Reinhard, Sengstag, Thierry, Serra-Picamal, Xavier, Spek, Wouter, Vaas, Lea A I, van Batenburg, Okker, Vandelaer, Marc, Varnai, Peter, Villoslada, Pablo, Vizcaíno, Juan Antonio, Wubbe, John Peter Mary, and Zanetti, Gianluigi

Published
2016

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