Beyond COVID

Risultati finali

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

Pubblicazioni

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

Autori: Goble, Carole; Soiland-Reyes, Stian
Pubblicato in: ZENODO, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7147703

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

Autori: Ramon; Delphine; Allyson; Milo; Susanna-Assunta
Pubblicato in: FAIRsharing, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7064637

Updating Linked Data practices for FAIR Digital Object principles

Autori: Stian Soiland-Reyes; Leyla Jael Castro; Daniel Garijo; Marc Portier; Carole Goble; Paul Groth
Pubblicato in: RIO, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7256428

Improving Galaxy provenance export using RO-Crate

Autori: Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Pubblicato in: GALAXY TRAINING, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7257146

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

Autori: Justin Clark-Casey; Stian Soiland-Reyes
Pubblicato in: ELIXIR, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7323480

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

Autori: Braukmann, Ricarda
Pubblicato in: DANS, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7867780

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

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

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

Autori: Mark D. Wilkinson; Susanna-Assunta Sansone; Eva Méndez; Romain David; Richard Dennis; David Hecker; Mari Kleemola; Carlo Lacagnina; Anastasija Nikiforova; Leyla Jael Castro
Pubblicato in: Open Research Europe, 2022, ISSN 2732-5121
Editore: 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

Autori: 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
Pubblicato in: bioRxiv, 2022, ISSN 2692-8205
Editore: 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

Autori: István Csabai, Krisztián Papp, Dávid Visontai et al.
Pubblicato in: Research Square, Numero V1, 2021, ISSN 2693-5015
Editore: Research Square
DOI: 10.21203/rs.3.rs-1177047/v1

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

Autori: Anikó Mentes, Krisztián Papp, Dávid Visontai, József Stéger, VEO Technical Working Group, István Csabai, Anna Medgyes-Horváth & Orsolya Anna Pipek
Pubblicato in: Scientific Reports, Numero 12, 2022, ISSN 2045-2322
Editore: Springer Nature
DOI: 10.1038/s41598-022-21953-3

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

Autori: Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
Pubblicato in: Bioinformatics Advances, Numero 3 (1), 2023, ISSN 2635-0041
Editore: Oxford University Press
DOI: 10.1093/bioadv/vbad045

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

Autori: Istvan Csabai, Norbert Solymosi
Pubblicato in: Research Square, 2022, ISSN 2693-5015
Editore: Research Square
DOI: 10.21203/rs.3.rs-1330800/v1

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

Autori: Fábio Madeira, Matt Pearce, Adrian R N Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez
Pubblicato in: Nucleic Acids Research, Numero 50, 2022, ISSN 1362-4962
Editore: Oxford Academic
DOI: 10.1093/nar/gkac240

Updating Linked Data practices for FAIR Digital Object principles

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

Lightweight Distributed Provenance Model for Complex Real–world Environments

Autori: Wittner, R., Mascia, C., Gallo, M. et al.
Pubblicato in: Scientific Data, 2022, ISSN 2052-4463
Editore: Springer Nature
DOI: 10.1038/s41597-022-01537-6

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

Autori: 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.
Pubblicato in: Learning Health Systems, 2023, ISSN 2379-6146
Editore: Wiley
DOI: 10.1002/lrh2.10365

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

Autori: 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
Pubblicato in: Molecular Biology and Evolution, Numero 39 (4), 2022, ISSN 1537-1719
Editore: 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

Autori: Axel Abelein, Simone Ciofi-Baffoni, Cecilia Mörman, Rakesh Kumar, Andrea Giachetti, Mario Piccioli, and Henrik Biverstål
Pubblicato in: JACS Au, Numero 2, 11, 2022, ISSN 2691-3704
Editore: American Chemical Society
DOI: 10.1021/jacsau.2c00438

Angewandte Chemie - International Edition

Autori: Berg, Hannes et al.
Pubblicato in: Angew Chem Int Ed Engl., Numero 63, 26, 2024, ISSN 1433-7851
Editore: Wiley-VCH
DOI: 10.1002/anie.202205858

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

Autori: Chiara, M., Horner, D.S., Ferrandi, E. et al.
Pubblicato in: Communications biology, 2023, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-023-04784-4

Ten Simple Rules for making a software tool workflow-ready

Autori: Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al.
Pubblicato in: PLoS Comput Biol, 2022, ISSN 1553-7358
Editore: 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.

Autori: F. Bisognin, F. Messina, O. Butera, C. Nisii, A. Mazzarelli, S. Cristino, M. R. Pascale, G. Lombardi, A. Cannas, P. Dal Monte
Pubblicato in: Microbiology Spectrum, Numero 10, 6, 2022, ISSN 2165-0497
Editore: 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

Autori: 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
Pubblicato in: No Journal Title, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7520086

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

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

BY-COVID M7.3: Industry sector mapping report

Autori: Lauer, Katharina; Smith, Andrew; Sousoni, Despoina; Westwick, Elaine; Martin, Corinne; Alloza Anguiano, Eva; David, Romain; Blomberg, Niklas
Pubblicato in: By-covid, 2023
Editore: 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?

Autori: Eržen, Ivan, Fafangel, Mario, Gabrovec, Branko, Selak, Špela, Skaza, Alenka, Vrdelja, Mitja
Pubblicato in: Nacionalni inštitut za javno zdravje, 2022
Editore: Nacionalni inštitut za javno zdravje

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

Autori: Westwick, Elaine; Haskell, Erin; Martin, Corinne
Pubblicato in: BEYOND COVID, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6884870

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

Autori: 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,
Pubblicato in: bioRxiv, 2023
Editore: bioRxiv
DOI: 10.1101/2023.04.19.537514

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

Autori: Willems, Marieke; Taverner, Ellie
Pubblicato in: BY-COVID, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7789351

BY-COVID - D8.2 - Data Management Plan

Autori: García Álvarez, Eva; Mayrhofer, Michaela; Holub, Peter
Pubblicato in: BEYOND COVID, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.6884816

BY-COVID D1.1 Extended workflows

Autori: Cochrane, Guy; Amid, Clara
Pubblicato in: BEYOND COVID, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.7875986

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

Autori: 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
Pubblicato in: Scientific data, Numero 10, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7156792

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

Autori: 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
Pubblicato in: BEYOND COVID, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7129553

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

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

Open data to support European pandemic preparedness.

Autori: 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
Pubblicato in: BY-COVID, 2023
Editore: 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

Autori: Canham, Steve; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria
Pubblicato in: BEYOND COVID, 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7064624

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

Autori: Estupiñán-Romero, Francisco; Launa-Garcés, Ramón; Van Dam, Iris; Cosgrove, Shona; Van Goethem, Nina; Bernal-Delgado, Enrique
Pubblicato in: Numero BEYOND COVID, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7944195

BY-COVID - D8.1 - Project Management Handbook

Autori: Arenas Marquez, Juan; Troncoso Quilaqueo, Andrea
Pubblicato in: BEYOND COVID, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.6884734

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

Autori: 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
Pubblicato in: BEYOND COVID, 2022
Editore: 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

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

BioHackEU22 Project 22: Plant data exchange and standard interoperability

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

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

Autori: Natalia Martínez-Lizaga; Marjan Meurisse; Francisco Estupiñan-Romero; Nina Van Goethem; Enrique Bernal-Delgado
Pubblicato in: BY COVID, 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7625784

Building a FAIR image data ecosystem for microscopy communities

Autori: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Pubblicato in: Histochemestry and Cell Biology, Numero 160, 2023, Pagina/e 199-209
Editore: Zenodo
DOI: 10.5281/zenodo.7788899

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