Beyond COVID

Livrables

Documentation on metadata standards for inclusion of resources in data portalLead beneficiary is TAUFSD an affiliated entity of CESSDA ERIC

D8.1.1 Project Handbook initial release and periodic updates

Initial version of the Project Handbook following Open PM2 best practices ELIXIR Hub

D8.4: BY-COVID Policy Brief I: Open data to support European pandemic preparedness

BY-COVID, being funded under the Horizon Europe programme, will deliver 2 policy briefs as deliverables, one at M20 and one at M36. WP8 will coordinate the delivery of two BY-COVID policy briefs

D7.1 Dissemination, exploitation and communication Plan

Mandatory deliverable highlighting the Dissemination Exploitation and Communication Plan ELIXIR Hub

D3.2 Tiered indexing system

Implementation of cloudbased high performance scalable indexing system EMBLEBI

D2.2. Data Access and Transfer across research domains and jurisdictions

Report describing technical legal and organisational barriers across data sources and identified solutions for data access including the procedures to manage users permissions for controlled access dataLead beneficiary is CRG an affiliated entity of BSC

D8.1.2 Project Handbook initial release and periodic updates.

Initial version of the Project Handbook following Open PM2 best practices ELIXIR Hub

D2.1 Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19

Report describing the initial infrastructure setup to enable COVID19 data access and transfer as well as the intradomain harmonisation for WP data sources Lead beneficiary is UNottingham an affiliated entity of BBMRIERIC

D1.1 Extended workflows

Details of the first wave of extensions and developments upon viral data processing computational workflows operating within the SARSCoV2 Data Hubs

Publications

RO-Crate: packaging metadata love notes into FAIR Digital Objects

Auteurs: Goble, Carole; Soiland-Reyes, Stian
Publié dans: ZENODO, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7147703

Semi-automatic mapping of external scientific databases into the FAIRsharing platform

Auteurs: Ramon; Delphine; Allyson; Milo; Susanna-Assunta
Publié dans: FAIRsharing, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7064637

Updating Linked Data practices for FAIR Digital Object principles

Auteurs: Stian Soiland-Reyes; Leyla Jael Castro; Daniel Garijo; Marc Portier; Carole Goble; Paul Groth
Publié dans: RIO, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7256428

Improving Galaxy provenance export using RO-Crate

Auteurs: Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Publié dans: GALAXY TRAINING, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7257146

Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories

Auteurs: Justin Clark-Casey; Stian Soiland-Reyes
Publié dans: ELIXIR, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7323480

The DANS Data Station Social Sciences & Humanities - Enabling FAIR data in the Dutch SSH community

Auteurs: Braukmann, Ricarda
Publié dans: DANS, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7867780

Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting

Auteurs: Stian Soiland-Reyes; Peter Sefton; Leyla Jael Castro; Frederik Coppens; Daniel Garijo; Simone Leo; Marc Portier; Paul Groth; Carole Goble
Publié dans: MANCHESTER 1824, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7243110

Community-driven governance of FAIRness assessment: an open issue, an open discussion

Auteurs: Mark D. Wilkinson; Susanna-Assunta Sansone; Eva Méndez; Romain David; Richard Dennis; David Hecker; Mari Kleemola; Carlo Lacagnina; Anastasija Nikiforova; Leyla Jael Castro
Publié dans: Open Research Europe, 2022, ISSN 2732-5121
Éditeur: European commission
DOI: 10.12688/openreseurope.15364.1

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

Auteurs: Ryan Connor, David A. Yarmosh, Wolfgang Maier, Migun Shakya, Ross Martin, Rebecca Bradford, J. Rodney Brister, Patrick SG Chain, Courtney A. Copeland, Julia di Iulio, Bin Hu, Philip Ebert, Jonathan Gunti, Yumi Jin, Kenneth S. Katz, Andrey Kochergin, Tré L
Publié dans: bioRxiv, 2022, ISSN 2692-8205
Éditeur: bioRxiv
DOI: 10.1101/2022.11.03.515010

Unique SARS-CoV-2 variant found in public sequence data of Antarctic soil samples collected in 2018-2019

Auteurs: István Csabai, Krisztián Papp, Dávid Visontai et al.
Publié dans: Research Square, Numéro V1, 2021, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-1177047/v1

Identification of mutations in SARS-CoV-2 PCR primer regions

Auteurs: Anikó Mentes, Krisztián Papp, Dávid Visontai, József Stéger, VEO Technical Working Group, István Csabai, Anna Medgyes-Horváth & Orsolya Anna Pipek
Publié dans: Scientific Reports, Numéro 12, 2022, ISSN 2045-2322
Éditeur: Springer Nature
DOI: 10.1038/s41598-022-21953-3

Mpox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Mpox

Auteurs: Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
Publié dans: Bioinformatics Advances, Numéro 3 (1), 2023, ISSN 2635-0041
Éditeur: Oxford University Press
DOI: 10.1093/bioadv/vbad045

Host genomes for the unique SARS-CoV-2 variant leaked into Antarctic soil metagenomic sequencing data

Auteurs: Istvan Csabai, Norbert Solymosi
Publié dans: Research Square, 2022, ISSN 2693-5015
Éditeur: Research Square
DOI: 10.21203/rs.3.rs-1330800/v1

Search and sequence analysis tools services from EMBL-EBI in 2022

Auteurs: Fábio Madeira, Matt Pearce, Adrian R N Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez
Publié dans: Nucleic Acids Research, Numéro 50, 2022, ISSN 1362-4962
Éditeur: Oxford Academic
DOI: 10.1093/nar/gkac240

Updating Linked Data practices for FAIR Digital Object principles

Auteurs: Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Publié dans: Research Ideas and Outcomes, 2022, ISSN 2367-7163
Éditeur: Pensoft Publishers
DOI: 10.3897/rio.8.e94501

Lightweight Distributed Provenance Model for Complex Real–world Environments

Auteurs: Wittner, R., Mascia, C., Gallo, M. et al.
Publié dans: Scientific Data, 2022, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/s41597-022-01537-6

Towards a common standard for data and specimen provenance in life sciences

Auteurs: Rudolf Wittner, Petr Holub, Cecilia Mascia, Francesca Frexia, Heimo Müller, Markus Plass, Clare Allocca, Fay Betsou, Tony Burdett, Ibon Cancio, Adriane Chapman, Martin Chapman, et al.
Publié dans: Learning Health Systems, 2023, ISSN 2379-6146
Éditeur: Wiley
DOI: 10.1002/lrh2.10365

Selection analysis identifies clusters of unusual mutational changes in Omicron lineage {BA}.1 that likely impact Spike function

Auteurs: Darren P. Martin, Spyros Lytras, Alexander G. Lucaci, Wolfgang Maier, Björn Grüning, Stephen D. Shank, Steven Weaver, Oscar A. MacLean, Richard J. Orton, Philippe Lemey, Maciej F. Boni, Houriiyah Tegally, Gordon W. Harkins, Cathrine Scheepers, Jinal N. Bh
Publié dans: Molecular Biology and Evolution, Numéro 39 (4), 2022, ISSN 1537-1719
Éditeur: Oxford University Press
DOI: 10.1093/molbev/msac061

Molecular Structure of Cu(II)-Bound Amyloid-β Monomer Implicated in Inhibition of Peptide Self-Assembly in Alzheimer’s Disease

Auteurs: Axel Abelein, Simone Ciofi-Baffoni, Cecilia Mörman, Rakesh Kumar, Andrea Giachetti, Mario Piccioli, and Henrik Biverstål
Publié dans: JACS Au, Numéro 2, 11, 2022, ISSN 2691-3704
Éditeur: American Chemical Society
DOI: 10.1021/jacsau.2c00438

Angewandte Chemie - International Edition

Auteurs: Berg, Hannes et al.
Publié dans: Angew Chem Int Ed Engl., Numéro 63, 26, 2024, ISSN 1433-7851
Éditeur: Wiley-VCH
DOI: 10.1002/anie.202205858

HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2

Auteurs: Chiara, M., Horner, D.S., Ferrandi, E. et al.
Publié dans: Communications biology, 2023, ISSN 2399-3642
Éditeur: Springer Nature
DOI: 10.1038/s42003-023-04784-4

Ten Simple Rules for making a software tool workflow-ready

Auteurs: Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al.
Publié dans: PLoS Comput Biol, 2022, ISSN 1553-7358
Éditeur: PLOS
DOI: 10.1371/journal.pcbi.1009823

Investigating the Origin of Mycobacterium chimaera Contamination in Heater-Cooler Units: Integrated Analysis with Fourier Transform Infrared Spectroscopy and Whole-Genome Sequencing.

Auteurs: F. Bisognin, F. Messina, O. Butera, C. Nisii, A. Mazzarelli, S. Cristino, M. R. Pascale, G. Lombardi, A. Cannas, P. Dal Monte
Publié dans: Microbiology Spectrum, Numéro 10, 6, 2022, ISSN 2165-0497
Éditeur: ASM Journals
DOI: 10.1128/spectrum.02893-22

Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

Auteurs: David, Romain; Richard, Audrey S.; Connellan, Claire; Lauer, Katharina B.; Chiusano, Maria Luisa; Goble, Carole; Houde, Martin; Kemmer, Isabel; Keppler, Antje; Lieutaud, Philippe; Ohmann, Christian; Panagiotopoulou, Maria; Raza Khan, Sara; Rybina, Arina; Soiland-Reyes, Stian; Wit, Charlotte; Wittner, Rudolf; Andrade Buono, Rafael; Marsh, Sarah Arnaud; Audergon, Pauline; Bonfils, Dylan; Carazo, Jose-Maria; Charrel, Remi; Coppens, Frederik; Fecke, Wolfgang; Filippone, Claudia; Garcia Alvarez, Eva; Gul, Sheraz; Hermjakob, Henning; Herzog, Katja; Holub, Petr; Kozera, Lukasz; Lister, Allyson L.; López-Coronado, José; Madon, Bénédicte; Majcen, Kurt; Martin, William; Müller, Wolfgang; Papadopoulou, Elli; Prat, Christine M.A.; Romano, Paolo; Sansone, Susanna-Assunta; Saunders, Gary; Blomberg, Niklas; Ewbank, Jonathan
Publié dans: No Journal Title, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7520086

BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment - Study protocol

Auteurs: Meurisse, Marjan; Van Goethem, Nina; Estupiñán-Romero, Francisco; González-Galindo, Javier; Royo-Sierra, Santiago; Martínez Lizaga, Natalia; Bernal-Delgado, Enrique
Publié dans: BEYOND COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7551182

BY-COVID M7.3: Industry sector mapping report

Auteurs: Lauer, Katharina; Smith, Andrew; Sousoni, Despoina; Westwick, Elaine; Martin, Corinne; Alloza Anguiano, Eva; David, Romain; Blomberg, Niklas
Publié dans: By-covid, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7186153

Zakaj je arhiviranje podatkov v času covid-19 pomembno? Why is data archiving important in the covid-19 era?

Auteurs: Eržen, Ivan, Fafangel, Mario, Gabrovec, Branko, Selak, Špela, Skaza, Alenka, Vrdelja, Mitja
Publié dans: Nacionalni inštitut za javno zdravje, 2022
Éditeur: Nacionalni inštitut za javno zdravje

BY-COVID - D7.1 - Communication, Dissemination and Exploitation Strategy

Auteurs: Westwick, Elaine; Haskell, Erin; Martin, Corinne
Publié dans: BEYOND COVID, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6884870

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Auteurs: Nadim Rahman, Colman O’Cathail, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Björn Grüning, Carla Cummins, Clara Amid, David Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae Prasad, Gábor Máté Gulyás, Gabriele Rinck, Jasmine McKinnon,
Publié dans: bioRxiv, 2023
Éditeur: bioRxiv
DOI: 10.1101/2023.04.19.537514

BY-COVID Deliverable 8.1.2 Project Handbook initial release and periodic updates

Auteurs: Willems, Marieke; Taverner, Ellie
Publié dans: BY-COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7789351

BY-COVID - D8.2 - Data Management Plan

Auteurs: García Álvarez, Eva; Mayrhofer, Michaela; Holub, Peter
Publié dans: BEYOND COVID, 2021
Éditeur: Zenodo
DOI: 10.5281/zenodo.6884816

BY-COVID D1.1 Extended workflows

Auteurs: Cochrane, Guy; Amid, Clara
Publié dans: BEYOND COVID, 2021
Éditeur: Zenodo
DOI: 10.5281/zenodo.7875986

The FAIR Cookbook - the essential resource for and by FAIR doers

Auteurs: Philippe Rocca-Serra; Wei Gu; Vassilios Ioannidis; Tooba Abbassi Daloii; Salvador Capella-Gutierrez; Ishwar Chandramouliswaran; Andrea Splendiani; Tony Burdett; Robert T. Giessmann; David Henderson; Dominique Batista; Allyson Lister; Ibrahim Emam; Yojana Gadiya; Lucas Giovanni; Egon Willighagen; Chris Evelo; Alasdair J. G. Gray; Philip Gribbon; Nick Juty; Danielle Welter; Karsten Quast; Paul Peeters; Herman van Vlijmen; Tom Plasterer; Dorothy Reilly; Eelke van der Horst; Susanna-Assunta Sansone; the FAIR Cookbook Recipes' Authors
Publié dans: Scientific data, Numéro 10, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7156792

BY-COVID D3.2: Implementation of cloud-based, high performance, scalable indexing system.

Auteurs: Hermjakob, Henning; Kleemola, Mari; Moilanen, Katja; Tuominen, Markus; Sansone, Susanna-Assunta; Lister, Allyson; David, Romain; Panagiotopoulou, Maria; Ohmann, Christian; Belien, Jeroen; Lischke, Julia; Juty, Nick; Soiland-Reyes, Stian
Publié dans: BEYOND COVID, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7129553

BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment preliminary outputs from Aragon, Spain

Auteurs: Estupiñán-Romero, Francisco; González-Galindo, Javier; Meurisse, Marjan; Martínez-Lizaga, Natalia; Royo-Sierra, Santiago; Van Goethem, Nina; Bernal-Delgado, Enrique
Publié dans: BY-COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7871534

Open data to support European pandemic preparedness.

Auteurs: Niklas Blomberg; Marieke Willems; Corinne S. Martin; Andy Smith; Elaine Harrison; Jose-Maria Carazo; Enrique Bernal-Delgado; Iris van Dam; Romain David; Patricia M. Palagi; Martina Draščić Capar
Publié dans: BY-COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7940608

Identification of COVID-19 clinical studies intending to share individual participant data for secondary use: Protocol for a pilot study

Auteurs: Canham, Steve; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria
Publié dans: BEYOND COVID, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7064624

BY-COVID Milestone 2.2 Mechanism for data access and use of routine real-world data

Auteurs: Estupiñán-Romero, Francisco; Launa-Garcés, Ramón; Van Dam, Iris; Cosgrove, Shona; Van Goethem, Nina; Bernal-Delgado, Enrique
Publié dans: Numéro BEYOND COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7944195

BY-COVID - D8.1 - Project Management Handbook

Auteurs: Arenas Marquez, Juan; Troncoso Quilaqueo, Andrea
Publié dans: BEYOND COVID, 2021
Éditeur: Zenodo
DOI: 10.5281/zenodo.6884734

BY-COVID - D3.1 - Metadata standards. Documentation on metadata standards for inclusion of resources in data portal

Auteurs: Hermjakob, Henning; Kleemola, Mari; Moilanen, Katja; Sansone, Susanna-Assunta; Lister, Allyson; David, Romain; Panagiotopoulou, Maria; Ohmann, Christian; Belien, Jeroen; Lischke, Julia; Juty, Nick; Soiland-Reyes, Stian
Publié dans: BEYOND COVID, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6885016

BY-COVID- D2.1 - Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19

Auteurs: Giles, Tom; Quinlan, Phil; Belien, Jeroen; Lischke, Julia; Portell-Silva, Laura; Capella-Gutierrez, Salvador; Karki, Reagon; Kalaitzi, Vasso; Bernal-Delgado, Enrique; Keppler, Antje
Publié dans: BEYOND COVID, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7017728

BioHackEU22 Project 22: Plant data exchange and standard interoperability

Auteurs: Arend, Daniel, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, et al.
Publié dans: BioHackrXiv Preprints, 2022
Éditeur: Center for Open Science
DOI: 10.37044/osf.io/c724r

BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment - Data Management Plan

Auteurs: Natalia Martínez-Lizaga; Marjan Meurisse; Francisco Estupiñan-Romero; Nina Van Goethem; Enrique Bernal-Delgado
Publié dans: BY COVID, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7625784

Building a FAIR image data ecosystem for microscopy communities

Auteurs: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publié dans: Histochemestry and Cell Biology, Numéro 160, 2023, Page(s) 199-209
Éditeur: Zenodo
DOI: 10.5281/zenodo.7788899

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