Beyond COVID

Deliverables

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

Author(s): Goble, Carole; Soiland-Reyes, Stian
Published in: ZENODO, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7147703

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

Author(s): Ramon; Delphine; Allyson; Milo; Susanna-Assunta
Published in: FAIRsharing, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7064637

Updating Linked Data practices for FAIR Digital Object principles

Author(s): Stian Soiland-Reyes; Leyla Jael Castro; Daniel Garijo; Marc Portier; Carole Goble; Paul Groth
Published in: RIO, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7256428

Improving Galaxy provenance export using RO-Crate

Author(s): Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Published in: GALAXY TRAINING, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7257146

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

Author(s): Justin Clark-Casey; Stian Soiland-Reyes
Published in: ELIXIR, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7323480

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

Author(s): Braukmann, Ricarda
Published in: DANS, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7867780

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

Author(s): Stian Soiland-Reyes; Peter Sefton; Leyla Jael Castro; Frederik Coppens; Daniel Garijo; Simone Leo; Marc Portier; Paul Groth; Carole Goble
Published in: MANCHESTER 1824, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7243110

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

Author(s): Mark D. Wilkinson; Susanna-Assunta Sansone; Eva Méndez; Romain David; Richard Dennis; David Hecker; Mari Kleemola; Carlo Lacagnina; Anastasija Nikiforova; Leyla Jael Castro
Published in: Open Research Europe, 2022, ISSN 2732-5121
Publisher: 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

Author(s): 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
Published in: bioRxiv, 2022, ISSN 2692-8205
Publisher: 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

Author(s): István Csabai, Krisztián Papp, Dávid Visontai et al.
Published in: Research Square, Issue V1, 2021, ISSN 2693-5015
Publisher: Research Square
DOI: 10.21203/rs.3.rs-1177047/v1

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

Author(s): Anikó Mentes, Krisztián Papp, Dávid Visontai, József Stéger, VEO Technical Working Group, István Csabai, Anna Medgyes-Horváth & Orsolya Anna Pipek
Published in: Scientific Reports, Issue 12, 2022, ISSN 2045-2322
Publisher: Springer Nature
DOI: 10.1038/s41598-022-21953-3

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

Author(s): Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
Published in: Bioinformatics Advances, Issue 3 (1), 2023, ISSN 2635-0041
Publisher: Oxford University Press
DOI: 10.1093/bioadv/vbad045

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

Author(s): Istvan Csabai, Norbert Solymosi
Published in: Research Square, 2022, ISSN 2693-5015
Publisher: Research Square
DOI: 10.21203/rs.3.rs-1330800/v1

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

Author(s): Fábio Madeira, Matt Pearce, Adrian R N Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez
Published in: Nucleic Acids Research, Issue 50, 2022, ISSN 1362-4962
Publisher: Oxford Academic
DOI: 10.1093/nar/gkac240

Updating Linked Data practices for FAIR Digital Object principles

Author(s): Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Published in: Research Ideas and Outcomes, 2022, ISSN 2367-7163
Publisher: Pensoft Publishers
DOI: 10.3897/rio.8.e94501

Lightweight Distributed Provenance Model for Complex Real–world Environments

Author(s): Wittner, R., Mascia, C., Gallo, M. et al.
Published in: Scientific Data, 2022, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-022-01537-6

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

Author(s): 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.
Published in: Learning Health Systems, 2023, ISSN 2379-6146
Publisher: Wiley
DOI: 10.1002/lrh2.10365

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

Author(s): 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
Published in: Molecular Biology and Evolution, Issue 39 (4), 2022, ISSN 1537-1719
Publisher: 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

Author(s): Axel Abelein, Simone Ciofi-Baffoni, Cecilia Mörman, Rakesh Kumar, Andrea Giachetti, Mario Piccioli, and Henrik Biverstål
Published in: JACS Au, Issue 2, 11, 2022, ISSN 2691-3704
Publisher: American Chemical Society
DOI: 10.1021/jacsau.2c00438

Angewandte Chemie - International Edition

Author(s): Berg, Hannes et al.
Published in: Angew Chem Int Ed Engl., Issue 63, 26, 2024, ISSN 1433-7851
Publisher: Wiley-VCH
DOI: 10.1002/anie.202205858

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

Author(s): Chiara, M., Horner, D.S., Ferrandi, E. et al.
Published in: Communications biology, 2023, ISSN 2399-3642
Publisher: Springer Nature
DOI: 10.1038/s42003-023-04784-4

Ten Simple Rules for making a software tool workflow-ready

Author(s): Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al.
Published in: PLoS Comput Biol, 2022, ISSN 1553-7358
Publisher: 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.

Author(s): F. Bisognin, F. Messina, O. Butera, C. Nisii, A. Mazzarelli, S. Cristino, M. R. Pascale, G. Lombardi, A. Cannas, P. Dal Monte
Published in: Microbiology Spectrum, Issue 10, 6, 2022, ISSN 2165-0497
Publisher: 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

Author(s): 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
Published in: No Journal Title, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7520086

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

Author(s): Meurisse, Marjan; Van Goethem, Nina; Estupiñán-Romero, Francisco; González-Galindo, Javier; Royo-Sierra, Santiago; Martínez Lizaga, Natalia; Bernal-Delgado, Enrique
Published in: BEYOND COVID, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7551182

BY-COVID M7.3: Industry sector mapping report

Author(s): Lauer, Katharina; Smith, Andrew; Sousoni, Despoina; Westwick, Elaine; Martin, Corinne; Alloza Anguiano, Eva; David, Romain; Blomberg, Niklas
Published in: By-covid, 2023
Publisher: 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?

Author(s): Eržen, Ivan, Fafangel, Mario, Gabrovec, Branko, Selak, Špela, Skaza, Alenka, Vrdelja, Mitja
Published in: Nacionalni inštitut za javno zdravje, 2022
Publisher: Nacionalni inštitut za javno zdravje

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

Author(s): Westwick, Elaine; Haskell, Erin; Martin, Corinne
Published in: BEYOND COVID, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6884870

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

Author(s): 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,
Published in: bioRxiv, 2023
Publisher: bioRxiv
DOI: 10.1101/2023.04.19.537514

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

Author(s): Willems, Marieke; Taverner, Ellie
Published in: BY-COVID, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7789351

BY-COVID - D8.2 - Data Management Plan

Author(s): García Álvarez, Eva; Mayrhofer, Michaela; Holub, Peter
Published in: BEYOND COVID, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.6884816

BY-COVID D1.1 Extended workflows

Author(s): Cochrane, Guy; Amid, Clara
Published in: BEYOND COVID, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.7875986

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

Author(s): 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
Published in: Scientific data, Issue 10, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7156792

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

Author(s): 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
Published in: BEYOND COVID, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7129553

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

Author(s): Estupiñán-Romero, Francisco; González-Galindo, Javier; Meurisse, Marjan; Martínez-Lizaga, Natalia; Royo-Sierra, Santiago; Van Goethem, Nina; Bernal-Delgado, Enrique
Published in: BY-COVID, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7871534

Open data to support European pandemic preparedness.

Author(s): 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
Published in: BY-COVID, 2023
Publisher: 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

Author(s): Canham, Steve; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria
Published in: BEYOND COVID, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7064624

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

Author(s): Estupiñán-Romero, Francisco; Launa-Garcés, Ramón; Van Dam, Iris; Cosgrove, Shona; Van Goethem, Nina; Bernal-Delgado, Enrique
Published in: Issue BEYOND COVID, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7944195

BY-COVID - D8.1 - Project Management Handbook

Author(s): Arenas Marquez, Juan; Troncoso Quilaqueo, Andrea
Published in: BEYOND COVID, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.6884734

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

Author(s): 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
Published in: BEYOND COVID, 2022
Publisher: 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

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

BioHackEU22 Project 22: Plant data exchange and standard interoperability

Author(s): Arend, Daniel, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, et al.
Published in: BioHackrXiv Preprints, 2022
Publisher: Center for Open Science
DOI: 10.37044/osf.io/c724r

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

Author(s): Natalia Martínez-Lizaga; Marjan Meurisse; Francisco Estupiñan-Romero; Nina Van Goethem; Enrique Bernal-Delgado
Published in: BY COVID, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7625784

Building a FAIR image data ecosystem for microscopy communities

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

Deliverables

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