Beyond COVID

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

D3.1 Metadata standards

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

Hands on social sciences data anonymization exercise

Auteurs: Vipavc Brvar, Irena
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.11123132

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

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

Auteurs: Kleemola, Mari
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.11066716

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

Auteurs: Simon Saldner, Sonja Bezjak, Vasso Kalaitzi, Kondyli Dimitra, Carola Schulz, Irena Vipavc. Brvar, Patricia M Palagi
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.11220597

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

Packing provenance using CPM RO-Crate profile

Auteurs: Rudolf Wittner, Matej Gallo, Simone Leo, Stian Soiland-Reyes
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7676924

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

Auteurs: 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
Publié dans: Numéro 11, 9, 2023
Éditeur: Microorganisms
DOI: 10.3390/microorganisms11092251

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

Auteurs: Garcia Alvarez, Eva; Holub, Petr; Colussi, Ilaria; Panagiotopoulou, Maria
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13981358

Introduction to Semantic Interoperability Challenges for RIs

Auteurs: David, Romain; Madon, Bénédicte; Torralba, Antonio
Publié dans: Zenodo, 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.8059821

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

Auteurs: Garcia Alvarez, Eva; Holub, Petr
Publié dans: 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.7476926

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

Auteurs: Nina Van Goethen; Marjan Meurisse; Javier González-Galindo; Natalia Martínez-Lizaga; Francisco Estupiñán-Romero; Enrique Bernal-Delgado
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7993140

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

Auteurs: Christian Ohmann; Maria Panagiotopoulou; Steve Canham; Gerd Felder; Pablo Emilio Verde
Publié dans: BMC Medical Research Methodology, Vol 24, Iss 1, Pp 1-11 (2024), 2024
Éditeur: BMC
DOI: 10.1186/s12874-024-02168-8

BY-COVID D1.2: Preparedness Data Hub

Auteurs: Rahman, Nadim; O'Cathail, Colman; Martiny, Hannah-Marie; Ventouratou, Marianna; Waheed, Zahra; Amid, Clara; Kleemola, Mari; Neves, Aitana
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.10069940

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

Auteurs: Neves, Aitana; Hjerde, Erik; Ventouratou, Marianna
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13946603

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

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

Auteurs: Ohmann, Christian; Moilanen, Katja; Kleemola, Mari; Canham, Steve; Panagiotopoulou, Maria
Publié dans: Crossref, 2023
Éditeur: /
DOI: 10.12688/openreseurope.16284.1

BY-COVID D6.1 Stakeholder engagement report

Auteurs: 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
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.12820912

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

Auteurs: Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas N Petersen, Oksana Lukjancenko, Frank M Aarestrup, Philip TLC Clausen, Patrick Munk
Publié dans: 2024
Éditeur: Bioinformatics
DOI: 10.1093/bioinformatics/btae086

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

Auteurs: Felder, Gerard; Contrino, Sergio; Ohmann, Christian; Panagiotopoulou, Maria; Matei, Mihaela; Kouylekov, Milen; Wolff, Russel Gene
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13981769

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

Auteurs: Willems, Marieke; Blomberg, Niklas; Maccallum, Peter; Tyler, Maria
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13920061

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Auteurs: Stian Soiland-Reyes; Carole Goble; Paul Groth
Publié dans: 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
Éditeur: PeerJ
DOI: 10.48550/arxiv.2306.07436

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

Auteurs: Sousoni, Despoina; Balsyte, Erika; Harrison, Elaine; Bäckman, Ulrika; Smith, Andrew
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13889809

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

Auteurs: 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
Publié dans: https://hal.science/hal-04149733, 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8101848

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

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

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

Auteurs: Rahman, Nadim; Zyoud, Ahman; Waheed, Zahra
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13323331

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

Auteurs: Van Goethem, Nina; Cavillot, Lisa
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7988733

Beyond Covid Educational Toolkit

Auteurs: Van Hoof, Wannes; Genten, Olivia
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.14025911

Toward 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; 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
Publié dans: Learning Health Systems, Vol 8, Iss 1, Pp n/a-n/a (2024), 2023
Éditeur: .
DOI: 10.5281/zenodo.5093124

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

Auteurs: Lavitrano, Marialuisa; Cocuzza, Clementina; Musumeci, Rosario
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13332781

The BeYond COVID project: STORIES OF SUCCESS

Auteurs: Harrison, Elaine; Maccallum, Peter
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.14499931

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 D8.1.3 Project Handbook initial release and periodic updates

Auteurs: Tyler, Maria; Fernandez Hidalgo, Maria Dolores
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13985857

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

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

Auteurs: 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
Publié dans: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024), 2023
Éditeur: /
DOI: 10.21203/rs.3.rs-3159433/v1

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

Auteurs: Van Goethem, Nina; Bernal-Delgado, Enrique; Estupiñán-Romero, Francisco; Meurisse, Marjan
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13870075

BY-COVID deliverable 4.2: Common analysis environment

Auteurs: Maier, Wolfgang; Rasche, Helena; Buono, Rafael Andrade
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.12706837

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

Auteurs: Regina Nora Fiam, Csabai Istvan, Solymosi Norbert
Publié dans: 2023
Éditeur: BioRxiv
DOI: 10.1101/2023.08.03.551784

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

Auteurs: Portell-Silva, Laura
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13981571

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

Auteurs: Belien, Jeroen
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7982090

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

The ODISSEI Portal: collecting metadata from Dutch data providers

Auteurs: Maineri, Angelica Maria
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.7970500

Recording provenance of workflow runs with RO-Crate

Auteurs: 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
Publié dans: 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
Éditeur: /
DOI: 10.48550/arxiv.2312.07852

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

BY-COVID D6.2 Training efforts report

Auteurs: Palagi, Patricia; Rahman, Nadim; Kleemola, Mari; Kalaitzi, Vasso; Saldner, Simon; Rasche, Helena; Kemmer, Isabel Marinna; Morgan, Sarah; Brvar, Irena Vipavc
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13349254

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

Auteurs: Maccallum, Peter; Hermjakob, Henning; Harrison, Elaine; Tseng, Yun-Yun
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.14001994

BY-COVID D4.1 Infectious Diseases Toolkit

Auteurs: Peterson, Hedi; Buono, Rafael Andrade; Portell Silva, Laura; Palagi, Patricia; Hughes, Liane; Droesbeke, Bert
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13909280

Antibiotic-Resistant ESKAPE Pathogens and COVID-19: The Pandemic beyond the Pandemic

Auteurs: Alessia Catalano, Domenico Iacopetta, Jessica ceramella, Michele Pellegrino, Federica Giuzio, Maria Marra, Camillo Rosano, Carmela Saturnino, Maria Stefania Sinicropi, Stefano Aquaro
Publié dans: 2023
Éditeur: Viruses
DOI: 10.3390/v15091843

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

Auteurs: Ostaszewski, Marek; Messina, Francesco; Mathur, Aastha; Kemmer, Isabel; Gribbon, Philip; Stubbs, Andrew; Rasche, Helena; Portell, Laura; Ene, Erdina; Hermjakob, Henning
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13330037

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

Auteurs: Cesare Ernesto Maria Gruber, Fabio Giovanni Tucci, Martina Rueca, Valentina Mazzotta, Giulia Gramigna et al
Publié dans: BIOMOLECULES, Numéro 13,10, 2023
Éditeur: Biomolecules
DOI: 10.3390/biom13101538

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

Auteurs: 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
Publié dans: BMC medical research methodology, Vol. 23, no.1, p. 248 [1-15] (2023), 2023
Éditeur: -
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

Auteurs: Christian Ohmann, Steve Canham, Kurt Majcen, Vittorio Meloni, Luca Pireddu, Alessandr Sulis, giovanni Delussu, Francesa Frexia, Petr Holub
Publié dans: 2024
Éditeur: European Commision

Building an interoperable Genomic Data Infrastructure

Auteurs: Coppens, Frederik
Publié dans: 2022
Éditeur: Zenodo
DOI: 10.5281/zenodo.6604464

BY-COVID D3.3.2 COVID-19 Data Portal

Auteurs: 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
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13332975

BY-COVID D4.3 Provenance model for infectious diseases

Auteurs: Wittner, Rudolf; Soiland-Reyes, Stian; Leo, Simone; Meurisse, Marjan; Hermjakob, Henning
Publié dans: 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
Éditeur: Zenodo
DOI: 10.5281/zenodo.10927253

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

Auteurs: Rambla, Jordi; Cortada, Aina Jené; Curwin, Amy
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.13255875

Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex

Auteurs: Maria Kuzikov, Jeanette Reinshagen, Krzysztof Wycisk, Angela Corona, Francesa Esposito, Paolo Malune, Candida Manelfi, Daniela Iaconis, Andrea Beccari, Enzo Tramontano, Marcin Nowotny, Bjorn Windshugel, Phili Gribbon, Andrea Zaliani
Publié dans: 2024
Éditeur: Virus Research
DOI: 10.1016/j.virusres.2024.199356

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

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

Auteurs: Katharina Lauer, Romain David, Jonathan Ewbank, Nina Van Goethem, Elaine Harrison,
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.10204209

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

Auteurs: Enrique Bernal-Delgado; Van Goethem, Nina
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.12636106

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

The European Nucleotide Archive in 2023

Auteurs: David Yuan, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan gupta, Vikas Gupta, et al
Publié dans: 2024
Éditeur: Nucleic Acids Research
DOI: 10.1093/nar/gkad1067

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

Auteurs: 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
Publié dans: 2023
Éditeur: 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

Auteurs: Van Goethem, Nina; Meurisse, Marjan; Estupiñán Romero, Francisco; Bernal-Delgado, Enrique; Saldner, Simon; Kalaitzi, Vasso
Publié dans: 2024
Éditeur: Zenodo
DOI: 10.5281/zenodo.12771703

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

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

Auteurs: Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Publié dans: 2023
Éditeur: New Biotechnology
DOI: 10.1016/j.nbt.2023.09.006

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

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

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

Auteurs: 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
Publié dans: Viruses, Numéro 15,11, 2023, ISSN 1999-4915
Éditeur: 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

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

Pharmacological profiles of neglected tropical disease drugs

Auteurs: Alessandro Greco; Reagon Karki; Yojana Gadiya; Clara Deecke; Andrea Zaliani; Sheraz Gul
Publié dans: Artificial Intelligence in the Life Sciences, 2024, ISSN 2667-3185
Éditeur: Elsevier
DOI: 10.1016/j.ailsci.2024.100116

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

Viruses

Auteurs: 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
Publié dans: Viruses, 2024, ISSN 1999-4915
Éditeur: MDPI
DOI: 10.3390/v16030430

Virus Research

Auteurs: 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
Publié dans: Virus Research, 2024, ISSN 0168-1702
Éditeur: 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

Auteurs: 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
Publié dans: Antibiotics, 2024, ISSN 2079-6382
Éditeur: MDPI AG
DOI: 10.3390/antibiotics13060561

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

RO-Crates Meets FAIR Digital Objects

Auteurs: Castro, Leyla Jael; Soiland-Reyes, Stian; Rebholz-Schuhmann, Dietrich
Publié dans: Proceedings of the Conference on Research Data Infrastructure, 2023, ISSN 2941-296X
Éditeur: TIB Open Publishing
DOI: 10.5281/zenodo.8348923

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

Auteurs: 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
Publié dans: Scientific Reports, 2022, ISSN 1476-4687
Éditeur: Scientific Reports
DOI: 10.1038/s41598-022-21953-3

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

Auteurs: Regina Nóra Fiam; Csabai István; Solymosi Norbert
Publié dans: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Éditeur: Oxford University Press
DOI: 10.1093/bib/bbae296

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

Viruses

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

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

Auteurs: Stian Soiland-Reyes; Leyla Jael Castro; Rohitha Ravinder; Claus Weiland; Jonas Grieb; Alexander Rogers; Christophe Blanchi; Herbert Van de Sompel
Publié dans: 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
Éditeur: BioHackrXiv
DOI: 10.37044/osf.io/gmk2h

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

Auteurs: Van Hoof, Wannes; Genten, Olivia; Kalaitzi, Vasso; Martin, Corinne
Publié dans: 2023
Éditeur: Zenodo
DOI: 10.5281/zenodo.8405780

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

Auteurs: 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
Publié dans: 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
Éditeur: Zenodo
DOI: 10.5281/zenodo.8386828

Recherche de données OpenAIRE...

Livrables

Publications

Partager cette page

Télécharger