Beyond COVID

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

D3.3.2 COVID-19 Data Portal

Continuously updated version of the COVID-19 Data Portal (EMBL-EBI).

D3.1 Metadata standards

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

D5.3b Hot Spot detection through wastewater surveillance and samples data collection

This deliverable will cover Hotspot detection through wastewater surveillance and samples data collection. Deliverable 5.3 has been split into 2 deliverables (D5.3a and D5.3b) as requested in the 1st amendment.Lead beneficiary is UNIMIB, an affiliated entity of BBMRI-ERIC.

D8.3 Report on sustainability plans

Sustainability plans for project outputs (ELIXIR Hub).

D8.5: BY-COVID Policy Brief II

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

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

D1.3 Tracking and open analytics tools

Details of the tracking and open analytics tools that support supervision and monitoring of the network of locally installed SARS-CoV-2 Data Hubs (EMBL-EBI).

D5.2 Secondary use of vaccine trial data and biosamples

This report will describe the secondary use of VACCELERATE clinical trial data and associated biosamples to measure the neutralising antibodies against emerging SARS-CoV-2 variants.

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

D1.2 Preparedness Data Hub

Details of tools to allow the rapid deployment and configuration of a disease X scenario preparedness Data Hub (EMBL-EBI).

D8.1.2 Project Handbook initial release and periodic updates.

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

D5.3a Mechanistic analyses via the COVID-19 Disease Map

Report about mechanistic analysis of COVID-19 or other pandemic prone pathogens. Deliverable has been split into 2 (D5.3a and D5.3b) as requested in the 1st amendment.Lead beneficiary is UNILU, an affiliated entity of ELIXIR/EMBL-EBI.

D4.3 Provenance model

A lightweight model for analysis transparency, sharing and trusted exchange.

D2.4. Report on data sources discovery and integration for enabling data use and re-use in response to future outbreaks

Report on the lessons learned, the WP2 infrastructure for data discovery and harmonisation, and the guidelines for managing future pandemics.

D6.1 Stakeholder engagement report

Building on the Milestone document (M06), this will be a high-level report summarising efforts and outcomes of stakeholder engagement across Tasks 6.1, 6.2 and 6.3 throughout project life, to include visuals and dissemination aspects (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

D7.3 Report on public engagement activities

Report analysing and assessing the effectiveness of the public engagement activities.

D1.4 The repurposing of 2 national SARS-CoV-2 data portals towards national pathogen portals

The repurposing of 2 national SARS-CoV-2 data portals towards national pathogen portals, focusing on vector-borne disease, via partners already involved in BY-COVID, namely the Swiss and Norwegian portals, following the Swedish pathogens portal example. A minimal set of functionalities would be developed that participating Portals would be required to provide through this work.

D5.1 Enriched report viral variants and health outcomes

Enriched on-line report on the impact of viral variants on health outcomes, once enriched with the new evidence generated in WP1 to WP3, and the outputs from the other use cases.

D6.2 The training efforts report

Building on the Milestone document (M6.2), this report will cover identified training needs, training events organised and produced training materials (of Task 6.4).

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

D2.3 Enabling data discovery at source using beacon-like mechanisms

Report describing existing data discovery mechanisms and the novel cross-domain data discovery via extensions to the Beacon and the Beacon Network technologies to non-genomics data.Lead beneficiary is CRG, an affiliated entity of BSC.

D3.3.1 COVID-19 Data Portal

Continuously updated version of the COVID-19 Data Portal (EMBL-EBI).

D7.2 Public report showcasing industry value from infectious disease data

Public report will showcase examples of success stories from companies using data from the project (ELIXIR Hub).

D8.1.3 Project Handbook initial release and periodic updates

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

D4.2 Common analysis environment

For the analysis and re-use of infectious diseases data.

D4.1 Infectious diseases toolkit

Toolkit with guidance to implement services for infectious diseases.Lead beneficiary is UT, an affiliated entity of ELIXIR Hub.

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

Hands on social sciences data anonymization exercise

Author(s): Vipavc Brvar, Irena
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.11123132

Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate

Author(s): Leo, Simone; Rodríguez-Navas, Laura; Fernández, José M.; De Geest, Paul; Pireddu, Luca; Crusoe, Michael R.; Garijo, Daniel; Colonnelli, Iacopo; Sirvent, Raül; Soiland-Reyes, Stian
Published in: F1000RESEARCH, 2023
Publisher: F1000RESEARCH
DOI: 10.5281/zenodo.8004793

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

How to make your sensitive data FAIR: use case in social sciences

Author(s): Kleemola, Mari
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.11066716

Data sharing and reuse under GDPR - BY-COVID Fest workshop report

Author(s): Simon Saldner, Sonja Bezjak, Vasso Kalaitzi, Kondyli Dimitra, Carola Schulz, Irena Vipavc. Brvar, Patricia M Palagi
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.11220597

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

Enhancing RDM in Galaxy by integrating RO-Crate

Author(s): Paul De Geest; Frederik Coppens; Stian Soiland-Reyes; Ignacio Eguinoa; Simone Leo
Published in: Research Ideas and Outcomes, 2022
Publisher: Research Ideas and Outcomes
DOI: 10.3897/rio.8.e95164

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

Packaging research artefacts with RO-Crate

Author(s): Peter Sefton; Mercè Crosas; Frederik Coppens; Marco La Rosa; Leyla Jael Castro; Carole Goble; Marc Portier; Eoghan Ó Carragáin; Björn Grüning; Paul Groth; RO-Crate Community; José M. Fernández; Simone Leo; Ana Trisovic; Stian Soiland-Reyes; Stian Soiland-Reyes; Daniel Garijo
Published in: Data Science, 2022, ISSN 2451-8484
Publisher: DATA SCIENCE
DOI: 10.48550/arxiv.2108.06503

Epidemiological and Molecular Investigation of the Heater–Cooler Unit (HCU)-Related Outbreak of Invasive Mycobacterium chimaera Infection Occurred in Italy

Author(s): Angela Cannas, Antonella Campanale, Daniela Minella, Francesco Messina, Ornella Butera, Carla Nisii, Antonio Mazzarelli, Carla Fontana, Lucia Lispi, Francesco Maraglino, Antonino Di Caro, Michela Sabbatucci
Published in: Microorganisms, Issue 11, 2023, ISSN 2076-2607
Publisher: MDPI AG
DOI: 10.3390/MICROORGANISMS11092251

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

Genomic and Epidemiologic Surveillance of SARS-CoV-2 in the Pandemic Period: Sequencing Network of the Lazio Region, Italy

Author(s): Martina Rueca, Giulia Berno, Alessandro Agresta, Martina Spaziante, Cesare Ernesto Maria Gruber, LAvinia Fabeni, Emanuela Giombini, Ornella Butera, Alessandra Barca, Paola Scognamiglio, Enrico Girardi, Fabrizio Maggi, Maria Beatrice Valli, Francesco Vairo
Published in: Viruses, Issue 15,11, 2023, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15112192

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, 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

Pharmacological profiles of neglected tropical disease drugs

Author(s): Alessandro Greco; Reagon Karki; Yojana Gadiya; Clara Deecke; Andrea Zaliani; Sheraz Gul
Published in: Artificial Intelligence in the Life Sciences, 2024, ISSN 2667-3185
Publisher: Elsevier
DOI: 10.1016/j.ailsci.2024.100116

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

Viruses

Author(s): Ryan Connor; Migun Shakya; David A. Yarmosh; Wolfgang Maier; Ross Martin; Rebecca Bradford; J. Rodney Brister; Patrick S. G. Chain; Courtney A. Copeland; Julia di Iulio; Bin Hu; Philip Ebert; Jonathan Gunti; Yumi Jin; Kenneth S. Katz; Andrey Kochergin; Tré LaRosa; Jiani Li; Po-E Li; Chien-Chi Lo; Sujatha Rashid; Evguenia S. Maiorova; Chunlin Xiao; Vadim Zalunin; Lisa Purcell; Kim D. Pruitt
Published in: Viruses, 2024, ISSN 1999-4915
Publisher: MDPI
DOI: 10.3390/v16030430

Virus Research

Author(s): Maria Kuzikov; Jeanette Reinshagen; Krzysztof Wycisk; Angela Corona; Francesca Esposito; Paolo Malune; Candida Manelfi; Daniela Iaconis; Andrea Beccari; Enzo Tramontano; Marcin Nowotny; Bjorn Windshügel; Philip Gribbon; Andrea Zaliani
Published in: Virus Research, 2024, ISSN 0168-1702
Publisher: Elsevier Amsterdam
DOI: 10.3204/pubdb-2024-05775

Screening of Klebsiella pneumoniae subsp. pneumoniae Strains with Multi-Drug Resistance and Virulence Profiles Isolated from an Italian Hospital between 2020 and 2023

Author(s): Valentina Dimartino; Carolina Venditti; Francesco Messina; Silvia D’Arezzo; Marina Selleri; Ornella Butera; Carla Nisii; Alessandra Marani; Alessia Arcangeli; Roberta Gaziano; Terenzio Cosio; Pietro Scanzano; Carla Fontana
Published in: Antibiotics, 2024, ISSN 2079-6382
Publisher: MDPI AG
DOI: 10.3390/antibiotics13060561

Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches

Author(s): Anna Niarakis; Anna Niarakis; Marek Ostaszewski; Alexander Mazein; Inna Kuperstein; Inna Kuperstein; Inna Kuperstein; Martina Kutmon; Marc E. Gillespie; Marc E. Gillespie; Akira Funahashi; Marcio Luis Acencio; Ahmed Hemedan; Michael Aichem; Karsten Klein; Tobias Czauderna; Felicia Burtscher; Takahiro G. Yamada; Yusuke Hiki; Noriko F. Hiroi; Noriko F. Hiroi; Finterly Hu; Finterly Hu; Nhung Pham; Nhung Pham; Friederike Ehrhart; Egon L. Willighagen; Alberto Valdeolivas; Aurelien Dugourd; Francesco Messina; Marina Esteban-Medina; Marina Esteban-Medina; Maria Peña-Chilet; Maria Peña-Chilet; Maria Peña-Chilet; Kinza Rian; Sylvain Soliman; Sara Sadat Aghamiri; Bhanwar Lal Puniya; Aurélien Naldi; Tomáš Helikar; Vidisha Singh; Marco Fariñas Fernández; Viviam Bermudez; Eirini Tsirvouli; Arnau Montagud; Vincent Noël; Vincent Noël; Vincent Noël; Miguel Ponce-de-Leon; Dieter Maier; Angela Bauch; Benjamin M. Gyori; John A. Bachman; Augustin Luna; Augustin Luna; Janet Piñero; Janet Piñero; Laura I. Furlong; Laura I. Furlong; Irina Balaur; Adrien Rougny; Adrien Rougny; Yohan Jarosz; Rupert W. Overall; Robert Phair; Livia Perfetto; Lisa Matthews; Devasahayam Arokia Balaya Rex; Marija Orlic-Milacic; Luis Cristobal Monraz Gomez; Luis Cristobal Monraz Gomez; Luis Cristobal Monraz Gomez; Bertrand De Meulder; Jean Marie Ravel; Jean Marie Ravel; Jean Marie Ravel; Bijay Jassal; Venkata Satagopam; Venkata Satagopam; Guanming Wu; Martin Golebiewski; Piotr Gawron; Laurence Calzone; Laurence Calzone; Laurence Calzone; Jacques S. Beckmann; Chris T. Evelo; Peter D’Eustachio; Falk Schreiber; Falk Schreiber; Julio Saez-Rodriguez; Joaquin Dopazo; Joaquin Dopazo; Joaquin Dopazo; Joaquin Dopazo; Martin Kuiper; Alfonso Valencia; Alfonso Valencia; Olaf Wolkenhauer; Olaf Wolkenhauer; Hiroaki Kitano; Emmanuel Barillot; Emmanuel Barillot; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; the COVID-19 Disease Map Community
Published in: Frontiers in Immunology, 2024, ISSN 1664-3224
Publisher: Frontiers in Immunology
DOI: 10.18452/28614

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

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

RO-Crates Meets FAIR Digital Objects

Author(s): Castro, Leyla Jael; Soiland-Reyes, Stian; Rebholz-Schuhmann, Dietrich
Published in: Proceedings of the Conference on Research Data Infrastructure, 2023, ISSN 2941-296X
Publisher: TIB Open Publishing
DOI: 10.5281/zenodo.8348923

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

Author(s): Mentes, Anikó; Papp, Krisztián; Visontai, Dávid; Stéger, József; Csabai, István; Papp, Krisztián; Visontai, Dávid; Stéger, József; Cochrane, Guy; Rahman, Nadim; Cummins, Carla; Yuan, David Yu; Selvakumar, Sandeep; Mansurova, Milena; O’Cathail, Colman; Sokolov, Alexey; Thorne, Ross; Koopmans, Marion; Nieuwenhuijse, David; Oude-Munnink, Bas; Worp, Nathalie; Amid, Clara; Csabai, István; Medgyes-Horváth, Anna; Pipek, Orsolya Anna
Published in: Scientific Reports, 2022, ISSN 1476-4687
Publisher: Scientific Reports
DOI: 10.1038/s41598-022-21953-3

Comparing full variation profile analysis with the conventional consensus method in SARS-CoV-2 phylogeny

Author(s): Regina Nóra Fiam; Csabai István; Solymosi Norbert
Published in: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbae296

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

Viruses

Author(s): Alessia Catalano; Domenico Iacopetta; Jessica Ceramella; Michele Pellegrino; Federica Giuzio; Maria Marra; Camillo Rosano; Carmela Saturnino; Maria Stefania Sinicropi; Stefano Aquaro
Published in: Viruses, 2023, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v15091843

BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas

Author(s): Stian Soiland-Reyes; Leyla Jael Castro; Rohitha Ravinder; Claus Weiland; Jonas Grieb; Alexander Rogers; Christophe Blanchi; Herbert Van de Sompel
Published in: Soiland-Reyes , S , Castro , L J , Ravinder , R , Weiland , C , Grieb , J , Rogers , A , Blanchi , C & Van de Sompel , H 2024 ' BioHackEU23 report: Enabling FAIR Digital Objects with RO-Crate, Signposting and Bioschemas ' BioHackrXiv , BioHackrXiv . https://doi.org/10.37044/osf.io/gmk2h, 2024, ISSN 0000-0000
Publisher: BioHackrXiv
DOI: 10.37044/osf.io/gmk2h

Packing provenance using CPM RO-Crate profile

Author(s): Rudolf Wittner, Matej Gallo, Simone Leo, Stian Soiland-Reyes
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7676924

"Preprint: ""Be Sustainable"", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons"

Author(s): David, Romain; Rybina, Arina; Burel, Jean-Marie; Heriche, Jean-Karim; Audergon, Pauline; Boiten, Jan-Willem; Coppens, Frederik; Crockett, Sara; Exter Katrina; Fahrener, Sven; Fratelli, Maddalena; Goble, Carole; Gormanns, Philipp; Grantner, Tobias; Gruning, Bjorn; Gurwitz, Kim Tamara; Hancock, John; Harmse, Henriette; Holub, Petr; Juty, Nick; Karnbach, Geoffrey; Karoune, Emma; Keppler, Antje; Klemeier, Jessica; Lancelotti, Carla; Legras, Jean-Luc; Lister, L. Allyson; Livio Longo, Dario; Ludwig, Rebecca; Madon, Benedicte; Massimi, Marzia; Matser, Vera; Matteoni, Rafaele; Mayrhofer, Michaela Th.; Ohmann , Christian; Panagiotopoulou, Maria; Parkinson, Helen; Perseil, Isabelle; Pfander, Claudia; Pieruschka, Roland; Raess, Michael; Rauber, Andreas; Richard, Audrey S.; Romano, Paolo; Rosato, Antonio; Sanchez-Pla, Alex; Sansone, Susanna-Assunta; Sarkans, Ugis; Serrano-Solano, Beatriz; Tang, Jing; Tanoli, Ziaurrehman; Tedds, Jonathan; Wagener, Harald; Weise, Martin; Westerhoff, Hans V.; Wittner, Rudolf; Ewbank, Jonathan; Blomberg, Niklas; Gribbon, Philip
Published in: Zenodo, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8226003

BY-COVID D8.2.3 Project Data Management Plan initial release and periodic updates

Author(s): Garcia Alvarez, Eva; Holub, Petr; Colussi, Ilaria; Panagiotopoulou, Maria
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13981358

Introduction to Semantic Interoperability Challenges for RIs

Author(s): David, Romain; Madon, Bénédicte; Torralba, Antonio
Published in: Zenodo, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.8059821

BY-COVID D8.2.2 Project Data Management Plan initial release and periodic updates M15

Author(s): Garcia Alvarez, Eva; Holub, Petr
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7476926

Continuously evolving demonstrator - Baseline use case: Prototyping a workflow that is standard to population health research

Author(s): Nina Van Goethen; Marjan Meurisse; Javier González-Galindo; Natalia Martínez-Lizaga; Francisco Estupiñán-Romero; Enrique Bernal-Delgado
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7993140

An assessment of the informative value of data sharing statements in clinical trial registries

Author(s): Christian Ohmann; Maria Panagiotopoulou; Steve Canham; Gerd Felder; Pablo Emilio Verde
Published in: BMC Medical Research Methodology, Vol 24, Iss 1, Pp 1-11 (2024), 2024
Publisher: BMC
DOI: 10.1186/s12874-024-02168-8

BY-COVID D1.2: Preparedness Data Hub

Author(s): Rahman, Nadim; O'Cathail, Colman; Martiny, Hannah-Marie; Ventouratou, Marianna; Waheed, Zahra; Amid, Clara; Kleemola, Mari; Neves, Aitana
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10069940

Euro-BioImaging's Template for Research Data Management Plans

Author(s): Kemmer, Isabel; Euro-BioImaging ERIC
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.11473803

BY-COVID D1.4 The repurposing of 2 national SARS-CoV-2 data portals towards national pathogen portals

Author(s): Neves, Aitana; Hjerde, Erik; Ventouratou, Marianna
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13946603

The European Nucleotide Archive in 2022

Author(s): Josephine Burgin; Alisha Ahamed; Carla Cummins; Rajkumar Devraj; Khadim Gueye; Dipayan Gupta; Vikas Gupta; Muhammad Haseeb; Maira Ihsan; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Balavenkataraman Kadhirvelu; Manish Kumar; Ankur Lathi; Rasko Leinonen; Milena Mansurova; Jasmine McKinnon; Colman O’Cathail; Joana Paupério; Stéphane Pesant; Nadim Rahman; Gabriele Rinck; Sandeep Selvakumar; Swati Suman; Senthilnathan Vijayaraja; Zahra Waheed; Peter Woollard; David Yuan; Ahmad Zyoud; Tony Burdett; Guy Cochrane
Published in: Nucleic Acids Research, 2022
Publisher: Pubmed
DOI: 10.1093/nar/gkac1051

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: 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: 2021
Publisher: Zenodo
DOI: 10.5281/ZENODO.7551182

ECRIN – CESSDA strategies for cross metadata mappings in selected areas between life sciences and social sciences and humanities

Author(s): Ohmann, Christian; Moilanen, Katja; Kleemola, Mari; Canham, Steve; Panagiotopoulou, Maria
Published in: Crossref, 2023
Publisher: /
DOI: 10.12688/openreseurope.16284.1

BY-COVID D6.1 Stakeholder engagement report

Author(s): Martin, Corinne; Balsyte, Erika; Guzmán Mesa, Andrea; Schulz, Carola; Sousoni, Despoina; Kalaitzi, Vasso; Saldner, Simon; Neves, Aitana; Kondyli, Dimitra; Vipavc Brvar, Irena; Carazo, José-María; Sánchez, Irene; Rosato, Antonio; Schutte, Nienke; Palagi, Patricia; Ventouratou, Marianna; Sansone, Susanna-Assunta; Natale, Alda; Dolanski-Aghamanoukjan, Lorenz
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.12820912

ARGprofiler—a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets

Author(s): Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas N Petersen, Oksana Lukjancenko, Frank M Aarestrup, Philip TLC Clausen, Patrick Munk
Published in: 2024
Publisher: Bioinformatics
DOI: 10.1093/bioinformatics/btae086

BY-COVID D5.2 Secondary use of vaccine trial data and biosamples

Author(s): Felder, Gerard; Contrino, Sergio; Ohmann, Christian; Panagiotopoulou, Maria; Matei, Mihaela; Kouylekov, Milen; Wolff, Russel Gene
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13981769

Instruct-ERIC Annual Report 2021

Author(s): Instruct-ERIC
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.6982942

Molecular Characterization of Multidrug-Resistant and Hypervirulent New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae in Lazio, Italy: A Five-Year Retrospective Study

Author(s): Claudia Rotondo; Carolina Venditti; Ornella Butera; Valentina Dimartino; Francesco Messina; Michele Properzi; Claudia Caparrelli; Valentina Antonelli; Silvia D’Arezzo; Marina Selleri; Carla Nisii; Carla Fontana; on behalf of the Lazio Region Laboratory Study Group
Published in: Antibiotics, 2024
Publisher: MDPI
DOI: 10.3390/ANTIBIOTICS13111045

BY-COVID D8.3 BY-COVID Long Term Sustainability Plan

Author(s): Willems, Marieke; Blomberg, Niklas; Maccallum, Peter; Tyler, Maria
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13920061

Instruct-ERIC Annual Report 2022

Author(s): Instruct-ERIC
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.13788988

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Author(s): Stian Soiland-Reyes; Carole Goble; Paul Groth
Published in: Soiland-Reyes , S , Goble , C & Groth , P 2023 , ' Evaluating FAIR Digital Object and Linked Data as distributed object systems ' , PeerJ Computer Science . https://doi.org/10.48550/arXiv.2306.07436, 2024
Publisher: PeerJ
DOI: 10.48550/arxiv.2306.07436

BY-COVID D7.2 - Report on industry value of infectious disease data

Author(s): Sousoni, Despoina; Balsyte, Erika; Harrison, Elaine; Bäckman, Ulrika; Smith, Andrew
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13889809

BY-COVID D2.2: Data Access and Transfer across research domains and jurisdictions

Author(s): Cortada, Aina Jené; Gormanns, Philipp; Furlani, Andrea; Van Dam, Iris; Portell-Silva, Laura; Belien, Jeroen; David, Romain; Navest, Robin; Heinonen, Matti; Tuominen, Markus; Kondyli, Dimitra; Freeberg, Mallory; Capella-Gutierrez, Salvador; Mathur, Aastha; Kleemola, Mari; Colussi, Ilaria; Giuffre, Carla; Blomberg, Niklas
Published in: https://hal.science/hal-04149733, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8101848

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, ISBN 978-961-6945-81-3
Publisher: Nacionalni inštitut za javno zdravje

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: Histochemistry and Cell Biology, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7788898

Instruct-ERIC Annual Report 2023

Author(s): Instruct-ERIC
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.13789052

BY-COVID D1.3. Tracking and open analytics tools

Author(s): Rahman, Nadim; Zyoud, Ahman; Waheed, Zahra
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13323331

Data landscape for infectious diseases surveillance in Belgium and use of socio-economic indicators

Author(s): Van Goethem, Nina; Cavillot, Lisa
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7988733

Beyond Covid Educational Toolkit

Author(s): Van Hoof, Wannes; Genten, Olivia
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.14025911

Toward 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; Mélanie Courtot; Vasa Curcin; Johann Eder; Mark Elliot; Katrina Exter; Carole Goble; Martin Golebiewski; Bron Kisler; Andreas Kremer; Simone Leo; Sheng Lin‐Gibson; Anna Marsano; Marco Mattavelli; Josh Moore; Hiroki Nakae; Isabelle Perseil; Ayat Salman; James Sluka; Stian Soiland‐Reyes; Caterina Strambio‐De‐Castillia; Michael Sussman; Jason R. Swedlow; Kurt Zatloukal; Jörg Geiger
Published in: Learning Health Systems, Vol 8, Iss 1, Pp n/a-n/a (2024), 2023
Publisher: .
DOI: 10.5281/zenodo.5093124

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 D5.3b Hot Spot detection through wastewater surveillance and samples data collection

Author(s): Lavitrano, Marialuisa; Cocuzza, Clementina; Musumeci, Rosario
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13332781

The BeYond COVID project: STORIES OF SUCCESS

Author(s): Harrison, Elaine; Maccallum, Peter
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.14499931

BY-COVID - D8.2 - Data Management Plan

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

Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development

Author(s): Berg, Hannes; Wirtz Martin, Maria A.; Altincekic, Nadide; Alshamleh, Islam; Kaur Bains, Jasleen; Blechar, Julius; Ceylan, Betül; de Jesus, Vanessa; Dhamotharan, Karthikeyan; Fuks, Christin; Gande, Santosh L.; Hargittay, Bruno; Hohmann, Katharina F.; Hutchison, Marie T.; Korn, Sophie Marianne; Krishnathas, Robin; Kutz, Felicitas; Linhard, Verena; Matzel, Tobias; Meiser, Nathalie; Bütikofer, Matthias; Ghosh, Dhiman; Riek, Roland; et al.
Published in: Angewandte Chemie. International Edition, 61 (46), 2022
Publisher: Angewandte Chemie. International Edition, 61 (46)
DOI: 10.3929/ethz-b-000577320

"EOSC-Future Test Science Project ""META-COVID"": Final report for CESSDA – ECRIN use case"

Author(s): Ohmann, Christian; Panagiotopoulou, Maria; Moilanen, Katja; Kleemola, Mari
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10014501

BY-COVID D8.1.3 Project Handbook initial release and periodic updates

Author(s): Tyler, Maria; Fernandez Hidalgo, Maria Dolores
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13985857

Sanitary Waters: Is It Worth Looking for Mycobacteria?

Author(s): Angela Cannas; Francesco Messina; Paola Dal Monte; Francesco Bisognin; Giorgio Dirani; Silvia Zannoli; Giulia Gatti; Ornella Butera; Vincenzo Ferraro; Carla Nisii; Elena Vecchi; Giovanna Mattei; Giuseppe Diegoli; Antonio Santoro; Gian Luigi Belloli; Enrico Girardi; Tiziana Lazzarotto; Vittorio Sambri; Carla Fontana
Published in: Microorganisms, 2024
Publisher: MDPI
DOI: 10.3390/microorganisms12101953

BY-COVID D1.1 Extended workflows

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

Provenance of specimen and data – A prerequisite for AI development in computational pathology

Author(s): Plass, Markus; Wittner, Rudolf; Holub, Petr; Frexia, Francesca; Mascia, Cecilia; Gallo, Matej; Müller, Heimo; Geiger, Jörg
Published in: New Biotechnology, 2023
Publisher: New Biotechnology
DOI: 10.1016/j.nbt.2023.09.006

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

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, 2024, ISSN 2379-6146
Publisher: Wiley
DOI: 10.1002/LRH2.10365

Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples

Author(s): Orsolya Anna Pipek; Anna Medgyes-Horváth; József Stéger; Krisztián Papp; Dávid Visontai; Marion Koopmans; David Nieuwenhuijse; Bas B. Oude Munnink; Guy Cochrane; Nadim Rahman; Carla Cummins; David Yu Yuan; Sandeep Selvakumar; Milena Mansurova; Colman O’Cathail; Alexey Sokolov; Ross Thorne; Nathalie Worp; Clara Amid; István Csabai
Published in: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024), 2023
Publisher: /
DOI: 10.21203/rs.3.rs-3159433/v1

BY-COVID D5.1 Enriched report viral variants and health outcomes

Author(s): Van Goethem, Nina; Bernal-Delgado, Enrique; Estupiñán-Romero, Francisco; Meurisse, Marjan
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13870075

BY-COVID deliverable 4.2: Common analysis environment

Author(s): Maier, Wolfgang; Rasche, Helena; Buono, Rafael Andrade
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.12706837

BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Local outputs and comparative analysis

Author(s): Meurisse, Marjan; Estupiñán-Romero, Francisco; Van Goethem, Nina; Perola, Markus; Paajanen, Teemu; González-Galindo, Javier; Bernal-Delgado, Enrique
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.11209362

BY-COVID D2.4 Report on data sources discovery and integration for enabling data use and re-use in response to future outbreaks

Author(s): Portell-Silva, Laura
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13981571

Health-RI COVID19 project Experiences and bottlenecks re: SSH data

Author(s): Belien, Jeroen
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7982090

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

The ODISSEI Portal: collecting metadata from Dutch data providers

Author(s): Maineri, Angelica Maria
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7970500

Recording provenance of workflow runs with RO-Crate

Author(s): Simone Leo; Michael R. Crusoe; Laura Rodríguez-Navas; Raül Sirvent; Alexander Kanitz; Paul De Geest; Rudolf Wittner; Luca Pireddu; Daniel Garijo; José M. Fernández; Iacopo Colonnelli; Matej Gallo; Tazro Ohta; Hirotaka Suetake; Salvador Capella-Gutierrez; Renske de Wit; Bruno P. Kinoshita; Stian Soiland-Reyes
Published in: Leo , S , Crusoe , M R , Rodríguez-Navas , L , Sirvent , R , Kanitz , A , Geest , P D , Wittner , R , Pireddu , L , Garijo , D , Fernández , J M , Colonnelli , I , Gallo , M , Ohta , T , Suetake , H , Capella-Gutierrez , S , Wit , R D , Kinoshita , B P & Soiland-Reyes , S 2024 , ' Recording provenance of workflow runs with RO-Crate ' , PLoS ONE . https://doi.org/10.48550/arXiv.2312.07852, 2023
Publisher: /
DOI: 10.48550/ARXIV.2312.07852

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: 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: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.7940608

BY-COVID D6.2 Training efforts report

Author(s): Palagi, Patricia; Rahman, Nadim; Kleemola, Mari; Kalaitzi, Vasso; Saldner, Simon; Rasche, Helena; Kemmer, Isabel Marinna; Morgan, Sarah; Brvar, Irena Vipavc
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13349254

Galaxy Training: A Powerful Framework for Teaching!

Author(s): Saskia Hiltemann; Helena Rasche; Simon Gladman; Hans-Rudolf Hotz; Delphine Larivière; Daniel Blankenberg; Pratik D Jagtap; Thomas Wollmann; Anthony Bretaudeau; Nadia Goué; Timothy J Griffin; Coline Royaux; Yvan Le Bras; Subina Mehta; Anna Syme; Frederik Coppens; Bert Droesbeke; Nicola Soranzo; Wendi Bacon; Fotis Psomopoulos; Cristóbal Gallardo-Alba; John Davis; Melanie Christine Föll; Matthias Fahrner; Maria A Doyle; Beatriz Serrano-Solano; Anne Claire Fouilloux; Peter van Heusden; Wolfgang Maier; Dave Clements; Florian Heyl; Galaxy Training Network; Björn Grüning; Bérénice Batut
Published in: PLOS Computational Biology, 2022
Publisher: PLOS Computational Biology
DOI: 10.1371/journal.pcbi.1010752

BY-COVID D8.5 Policy Brief II: Research data infrastructure for sustainable global pandemic preparedness

Author(s): Maccallum, Peter; Hermjakob, Henning; Harrison, Elaine; Tseng, Yun-Yun
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.14001994

BY-COVID D4.1 Infectious Diseases Toolkit

Author(s): Peterson, Hedi; Buono, Rafael Andrade; Portell Silva, Laura; Palagi, Patricia; Hughes, Liane; Droesbeke, Bert
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13909280

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 D5.3a Mechanistic analyses via the COVID-19 Disease Map

Author(s): Ostaszewski, Marek; Messina, Francesco; Mathur, Aastha; Kemmer, Isabel; Gribbon, Philip; Stubbs, Andrew; Rasche, Helena; Portell, Laura; Ene, Erdina; Hermjakob, Henning
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13330037

Treatment-Emergent Cilgavimab Resistance Was Uncommon in Vaccinated Omicron BA.4/5 Outpatients

Author(s): Cesare Ernesto Maria Gruber, Fabio Giovanni Tucci, Martina Rueca, Valentina Mazzotta, Giulia Gramigna et al
Published in: BIOMOLECULES, Issue 13,10, 2023
Publisher: Biomolecules
DOI: 10.3390/biom13101538

Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment

Author(s): Meurisse, Marjan; Estupiñán-Romero, Francisco; González-Galindo, Javier; Martínez-Lizaga, Natalia; Royo-Sierra, Santiago; Saldner, Simon; Dolanski-Aghamanoukjan, Lorenz; Degelsegger-Marquez, Alexander; Soiland-Reyes, Stian; Van Goethem, Nina; Bernal-Delgado, Enrique; BeYond-COVID project
Published in: BMC medical research methodology, Vol. 23, no.1, p. 248 [1-15] (2023), 2023
Publisher: -
DOI: 10.1186/s12874-023-02068-3

Linking the ECRIN Metadata Repository with the BBMRI-ERIC Directory to connect clinical studies with related biobanks and collections

Author(s): Christian Ohmann, Steve Canham, Kurt Majcen, Vittorio Meloni, Luca Pireddu, Alessandr Sulis, giovanni Delussu, Francesa Frexia, Petr Holub
Published in: 2024
Publisher: European Commision

Building an interoperable Genomic Data Infrastructure

Author(s): Coppens, Frederik
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6604464

BY-COVID D3.3.2 COVID-19 Data Portal

Author(s): Hermjakob, Henning; Kleemola, Mari; Sansone, Susanna-Assunta; Belien, Jeroen; David, Romain; Goble, Carole; Navest, Robin; Pearce, Matt; Panagiotopoulou, Maria; Guerin, Philippe; Kennon, Kalynn; Narain, Charvy
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13332975

BY-COVID D4.3 Provenance model for infectious diseases

Author(s): Wittner, Rudolf; Soiland-Reyes, Stian; Leo, Simone; Meurisse, Marjan; Hermjakob, Henning
Published in: Wittner , R , Soiland-Reyes , S , Leo , S , Meurisse , M & Hermjakob , H 2024 , BY-COVID D4.3 Provenance model for infectious diseases . Zenodo . https://doi.org/10.5281/zenodo.10927253, 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.10927253

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: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.7944195

BY-COVID D2.3 Enabling data discovery at source using beacon-like mechanisms

Author(s): Rambla, Jordi; Cortada, Aina Jené; Curwin, Amy
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.13255875

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

Beyond COVID - how the BY-COVID project is increasing European pandemic preparedness

Author(s): Katharina Lauer, Romain David, Jonathan Ewbank, Nina Van Goethem, Elaine Harrison,
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.10204209

BY-COVID D2.3 Enabling data discovery at source using beacon-like mechanisms

Author(s): Rambla, Jordi; Cortada, Aina Jené; Curwin, Amy
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/ZENODO.13255875

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

Author(s): Enrique Bernal-Delgado; Van Goethem, Nina
Published in: 2024
Publisher: Zenodo
DOI: 10.5281/zenodo.12636106

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

The European Nucleotide Archive in 2023

Author(s): David Yuan, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan gupta, Vikas Gupta, et al
Published in: 2024
Publisher: Nucleic Acids Research
DOI: 10.1093/nar/gkad1067

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 Spring 23 Use Cases Workshop: Integration of socioeconomic data in observational studies on vaccine effectiveness

Author(s): Kalaitzi, Vasso; van Goethem, Nina; Bernal Delgado, Enrique; Estupiñán-Romero, Francisco; Belien, Jeroen; Navest, Robin; Van Dam, Iris; Van Den Borre, Laura; Hof, Cees; Dillo, Ingrid; Cavillot, Lisa; Bezuidenhout, Louise; Knol, Mirjam; Genten, Olivia; Hubin, Pierre; Cosgrove, Shona; Saldner, Simon
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8234104

BY-COVID - WP5 - Baseline Use Case: Integration of socioeconomic data in observational studies using a prototyped workflow standard to federated population health research

Author(s): Van Goethem, Nina; Meurisse, Marjan; Estupiñán Romero, Francisco; Bernal-Delgado, Enrique; Saldner, Simon; Kalaitzi, Vasso
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/ZENODO.12771703

Provenance of specimen and data – A prerequisite for AI development in computational pathology

Author(s): Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Published in: 2023
Publisher: New Biotechnology
DOI: 10.1016/j.nbt.2023.09.006

Sustainability of FAIR Life Science Resources and Projects: Lessons Learned from EOSC-Life Research Infrastructures

Author(s): David, Romain; Burel, Jean-Marie; Heriche, Jean-Karim; Rybina, Arina; Audergon, Pauline; Boiten, Jan-Willem; Coppens, Frederik; Crockett, Sara; Exter Katrina; Fahrener, Sven; Fratelli, Maddalena; Goble, Carole; Gormanns, Philipp; Grantner, Tobias; Gruning, Bjorn; Gurwitz, Kim Tamara; Hancock, John; Harmse, Henriette; Holub, Petr; Juty, Nick; Karnbach, Geoffrey; Karoune, Emma; Keppler, Antje; Klemeier, Jessica; Lancelotti, Carla; Legras, Jean-Luc; Lister, L. Allyson; Livio Longo, Dario; Ludwig, Rebecca; Madon, Benedicte; Massimi, Marzia; Matser, Vera; Matteoni, Rafaele; Mayrhofer, Michaela Th.; Ohmann , Christian; Panagiotopoulou, Maria; Parkinson, Helen; Perseil, Isabelle; Pfander, Claudia; Pieruschka, Roland; Raess, Michael; Rauber, Andreas; Richard, Audrey S.; Romano, Paolo; Rosato, Antonio; Sanchez-Pla, Alex; Sansone, Susanna-Assunta; Sarkans, Ugis; Serrano-Solano, Beatriz; Tang, Jing; Tanoli, Ziaurrehman; Tedds, Jonathan; Wagener, Harald; Weise, Martin; Westerhoff, Hans V.; Wittner, Rudolf; Ewbank, Jonathan; Blomberg, Niklas; Gribbon, Philip
Published in: Zenodo, 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.8068648

BY-COVID D7.3: Report on public engagement activities

Author(s): Van Hoof, Wannes; Genten, Olivia; Kalaitzi, Vasso; Martin, Corinne
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8405780

BY-COVID D3.3.1: COVID-19 Data Portal

Author(s): Hermjakob, Henning; Kleemola, Mari; Ventouratou, Marianna; Lister, Allyson; Sansone, Susanna-Assunta; David, Romain; Lischke, Julia; Navest, Robin; Belien, Jeroen; Juty, Nick; Soiland-Reyes, Stian; Goble, Carole
Published in: Hermjakob , H , Kleemola , M , Ventouratou , M , Lister , A , Sansone , S-A , David , R , Lischke , J , Navest , R , Belien , J , Juty , N , Soiland-Reyes , S & Goble , C 2023 , BY-COVID D3.3.1: COVID-19 Data Portal . Zenodo . https://doi.org/10.5281/zenodo.8386828, 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8386828

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