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1. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

Abstract A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.

Published
2024
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2. Author Correction: The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Ann M. Mc Cartney, Giulio Formenti, Alice Mouton, Diego De Panis, Luísa S. Marins, Henrique G. Leitão, Genevieve Diedericks, Joseph Kirangwa, Marco Morselli, Judit Salces-Ortiz, Nuria Escudero, Alessio Iannucci, Chiara Natali, Hannes Svardal, Rosa Fernández, Tim De Pooter, Geert Joris, Mojca Strazisar, Jonathan M. D. Wood, Katie E. Herron, Ole Seehausen, Phillip C. Watts, Felix Shaw, Robert P. Davey, Alice Minotto, José M. Fernández, Astrid Böhne, Carla Alegria, Tyler Alioto, Paulo C. Alves, Isabel R. Amorim, Jean-Marc Aury, Niclas Backstrom, Petr Baldrian, Laima Baltrunaite, Endre Barta, Bertrand BedHom, Caroline Belser, Johannes Bergsten, Laurie Bertrand, Helena Bilandija, Mahesh Binzer-Panchal, Iliana Bista, Mark Blaxter, Paulo A. V. Borges, Guilherme Borges Dias, Mirte Bosse, Tom Brown, Rémy Bruggmann, Elena Buena-Atienza, Josephine Burgin, Elena Buzan, Alessia Cariani, Nicolas Casadei, Matteo Chiara, Sergio Chozas, Fedor Čiampor, Angelica Crottini, Corinne Cruaud, Fernando Cruz, Love Dalen, Alessio De Biase, Javier del Campo, Teo Delic, Alice B. Dennis, Martijn F. L. Derks, Maria Angela Diroma, Mihajla Djan, Simone Duprat, Klara Eleftheriadi, Philine G. D. Feulner, Jean-François Flot, Giobbe Forni, Bruno Fosso, Pascal Fournier, Christine Fournier-Chambrillon, Toni Gabaldon, Shilpa Garg, Carmela Gissi, Luca Giupponi, Jessica Gomez-Garrido, Josefa González, Miguel L. Grilo, Björn Grüning, Thomas Guerin, Nadege Guiglielmoni, Marta Gut, Marcel P. Haesler, Christoph Hahn, Balint Halpern, Peter W. Harrison, Julia Heintz, Maris Hindrikson, Jacob Höglund, Kerstin Howe, Graham M. Hughes, Benjamin Istace, Mark J. Cock, Franc Janžekovič, Zophonias O. Jonsson, Sagane Joye-Dind, Janne J. Koskimäki, Boris Krystufek, Justyna Kubacka, Heiner Kuhl, Szilvia Kusza, Karine Labadie, Meri Lähteenaro, Henrik Lantz, Anton Lavrinienko, Lucas Leclère, Ricardo Jorge Lopes, Ole Madsen, Ghislaine Magdelenat, Giulia Magoga, Tereza Manousaki, Tapio Mappes, Joao Pedro Marques, Gemma I. Martinez Redondo, Florian Maumus, Shane A. McCarthy, Hendrik-Jan Megens, Jose Melo-Ferreira, Sofia L. Mendes, Matteo Montagna, Joao Moreno, Mai-Britt Mosbech, Mónica Moura, Zuzana Musilova, Eugene Myers, Will J. Nash, Alexander Nater, Pamela Nicholson, Manuel Niell, Reindert Nijland, Benjamin Noel, Karin Noren, Pedro H. Oliveira, Remi-Andre Olsen, Lino Ometto, Rebekah A. Oomen, Stephan Ossowski, Vaidas Palinauskas, Snaebjorn Palsson, Jerome P. Panibe, Joana Pauperio, Martina Pavlek, Emilie Payen, Julia Pawlowska, Jaume Pellicer, Graziano Pesole, Joao Pimenta, Martin Pippel, Anna Maria Pirttilä, Nikos Poulakakis, Jeena Rajan, Rúben M.C. Rego, Roberto Resendes, Philipp Resl, Ana Riesgo, Patrik Rodin-Morch, Andre E. R. Soares, Carlos Rodriguez Fernandes, Maria M. Romeiras, Guilherme Roxo, Lukas Rüber, Maria Jose Ruiz-Lopez, Urmas Saarma, Luis P. da Silva, Manuela Sim-Sim, Lucile Soler, Vitor C. Sousa, Carla Sousa Santos, Alberto Spada, Milomir Stefanovic, Viktor Steger, Josefin Stiller, Matthias Stöck, Torsten H. Struck, Hiranya Sudasinghe, Riikka Tapanainen, Christian Tellgren-Roth, Helena Trindade, Yevhen Tukalenko, Ilenia Urso, Benoit Vacherie, Steven M. Van Belleghem, Kees Van Oers, Carlos Vargas-Chavez, Nevena Velickovic, Noel Vella, Adriana Vella, Cristiano Vernesi, Sara Vicente, Sara Villa, Olga Vinnere Pettersson, Filip A. M. Volckaert, Judit Voros, Patrick Wincker, Sylke Winkler, Claudio Ciofi, Robert M. Waterhouse, and Camila J. Mazzoni

Subjects
General. Including nature conservation, geographical distribution, QH1-199.5
Published
2024
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3. COPO - Managing sample metadata for biodiversity: considerations from the Darwin Tree of Life project [version 3; peer review: 2 approved, 1 approved with reservations]

Author

Guy Cochrane, Estelle Kilias, Felix Shaw, Josephine Burgin, Mara K.N. Lawniczak, Seanna McTaggart, Alice Minotto, Aaliyah Providence, Joana Paupério, Peter Harrison, Robert Davey, and Jeena Rajan

Subjects
biodiversity, standards, sharing, metadata, samples, Darwin Tree of Life, eng, Medicine, Science
Abstract

Large-scale reference genome sequencing projects for all of biodiversity are underway and common standards have been in place for some years to enable the understanding and sharing of sequence data. However, the metadata that describes the collection, processing and management of samples, and link to the associated sequencing and genome data, are not yet adequately developed and standardised for these projects. At the time of writing, the Darwin Tree of Life (DToL) Project is over two years into its ten-year ambition to sequence all described eukaryotic species in Britain and Ireland. We have sought consensus from a wide range of scientists across taxonomic domains to determine the minimal set of metadata that we collectively deem as critically important to accompany each sequenced specimen. These metadata are made available throughout the subsequent laboratory processes, and once collected, need to be adequately managed to fulfil the requirements of good data management practice. Due to the size and scale of management required, software tools are needed. These tools need to implement rigorous development pathways and change management procedures to ensure that effective research data management of key project and sample metadata is maintained. Tracking of sample properties through the sequencing process is handled by Lab Information Management Systems (LIMS), so publication of the sequenced data is achieved via technical integration of LIMS and data management tools. Discussions with community members on how metadata standards need to be managed within large-scale programmes is a priority in the planning process. Here we report on the standards we developed with respect to a robust and reusable mechanism of metadata collection, in the hopes that other projects forthcoming or underway will adopt these practices for metadata.

Published
2024
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4. A DNA barcoding framework for taxonomic verification in the Darwin Tree of Life Project [version 1; peer review: 2 approved]

Author

Silvia Salatino, Rebekka Uhl, Peter O. Mulhair, Freja Azzopardi, Jordan Beasley, Alex D. Twyford, Lucia Campos-Dominguez, Michelle L. Hart, Olga Sivell, David Bell, Gavin Broad, Felix Shaw, Piotr Cuber, Darren Choonea, Peter M. Hollingsworth, Laura L. Forrest, Sahr Mian, Alexandra Dombrowski, Mara K.N. Lawniczak, Claire Griffin, Clementine Greeves, Peter W.H. Holland, Joanna Harley, Owen T. Lewis, Amanda Jones, Ben W. Price, Raju Misra, Estelle Kilias, Ian Barnes, Laura Sivess, Heather Allen, Alice Minotto, Inez Januszczak, Michael Cunliffe, Mark L. Blaxter, Liam Crowley, Lyndall Pereira da Conceicoa, Brian Douglas, Kieran Woof, Ester Gaya, and Paul Kersey

Subjects
DNA barcoding, species identification, taxonomy, Britain and Ireland, biodiversity, eng, Medicine, Science
Abstract

Biodiversity genomics research requires reliable organismal identification, which can be difficult based on morphology alone. DNA-based identification using DNA barcoding can provide confirmation of species identity and resolve taxonomic issues but is rarely used in studies generating reference genomes. Here, we describe the development and implementation of DNA barcoding for the Darwin Tree of Life Project (DToL), which aims to sequence and assemble high quality reference genomes for all eukaryotic species in Britain and Ireland. We present a standardised framework for DNA barcode sequencing and data interpretation that is then adapted for diverse organismal groups. DNA barcoding data from over 12,000 DToL specimens has identified up to 20% of samples requiring additional verification, with 2% of seed plants and 3.5% of animal specimens subsequently having their names changed. We also make recommendations for future developments using new sequencing approaches and streamlined bioinformatic approaches.

Published
2024
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5. Colombia's cyberinfrastructure for biodiversity: Building data infrastructure in emerging countries to foster socioeconomic growth

Author

Jose J. De Vega, Robert P. Davey, Jorge Duitama, Dairo Escobar, Marco A. Cristancho‐Ardila, Graham J. Etherington, Alice Minotto, Nelson E. Arenas‐Suarez, Juan D. Pineda‐Cardenas, Javier Correa‐Alvarez, Anyela V. Camargo Rodriguez, Wilfried Haerty, Juan P. Mallarino‐Robayo, Emiliano Barreto‐Hernandez, Monica Muñoz‐Torres, Narcis Fernandez‐Fuentes, Federica Di Palma, and the Colombian Cyberinfrastructure Consortium for Biodiversity

Subjects
biodiversity, data management, e‐infrastructure, innovation, research policy, Environmental sciences, GE1-350, Botany, QK1-989
Abstract

Societal Impact Statement Colombia is a “megadiverse” country with vast natural resources. A history of recent conflict means that information is only now being collected on the natural capital of regions that were previously unexplored. Better access to data, tools, and expertise is required for evidence‐supported decisions on the conservation of these resources. The development of a bespoke cyberinfrastructure could help fulfill this need by providing access to digital resources in a collaborative cyberenvironment. We outline key priorities and develop a reference framework for building cyberinfrastructure in Colombia. This framework could be applied to other fields and countries to promote knowledge exchange, scientific innovation, and socioeconomic growth.

Published
2020
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6. COPO: a metadata platform for brokering FAIR data in the life sciences

Author

Paul J. Kersey, Alejandra Gonzalez-Beltran, Susanna-Assunta Sansone, Alice Minotto, Anthony Etuk, Philippe Rocca-Serra, Medha Devare, Felix Shaw, Elizabeth Arnaud, Marie-Angélique Laporte, Robert P. Davey, and David Johnson

Subjects
0301 basic medicine, Open science, Computer science, Process (engineering), Annotation, Data management, Interoperability, Omics, Reuse, Ontology (information science), Repositories, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Open Science, 0302 clinical medicine, Open Data, Ontologies, Information system, General Pharmacology, Toxicology and Pharmaceutics, 030304 developmental biology, Bioinformatics (Computational Biology), 0303 health sciences, General Immunology and Microbiology, Ontology, business.industry, Multi Omics, Repository, General Medicine, Genomics, Data science, Metadata, Open data, Open Standards, 030104 developmental biology, Science research, Open standard, Publishing, Bioinformatik (beräkningsbiologi), Schemas, business, 030217 neurology & neurosurgery
Abstract

Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but these are not typically trained in good data management practices. That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy. In response, recognition of the FAIR Principles (that data should be Findable, Accessible, Interoperable and Reusable) has become commonplace. However, both technical and cultural challenges for the implementation of these principles still exist when storing, managing, analysing and disseminating both legacy and new data.COPO is a computational system that attempts to address some of these challenges by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share it with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible. Building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing.AvailabilityCOPO is entirely open source and freely available on GitHub at https://github.com/collaborative-open-plant-omics. A public instance of the platform for use by the community, as well as more information, can be found at copo-project.org.

Published
2019
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