Beyond COVID

CORDIS proporciona enlaces a los documentos públicos y las publicaciones de los proyectos de los programas marco HORIZONTE.

Los enlaces a los documentos y las publicaciones de los proyectos del Séptimo Programa Marco, así como los enlaces a algunos tipos de resultados específicos, como conjuntos de datos y «software», se obtienen dinámicamente de OpenAIRE .

Resultado final

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

Publicaciones

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

Autores: Goble, Carole; Soiland-Reyes, Stian
Publicado en: ZENODO, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7147703

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

Autores: Ramon; Delphine; Allyson; Milo; Susanna-Assunta
Publicado en: FAIRsharing, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7064637

Updating Linked Data practices for FAIR Digital Object principles

Autores: Stian Soiland-Reyes; Leyla Jael Castro; Daniel Garijo; Marc Portier; Carole Goble; Paul Groth
Publicado en: RIO, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7256428

Improving Galaxy provenance export using RO-Crate

Autores: Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Publicado en: GALAXY TRAINING, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7257146

Hands on social sciences data anonymization exercise

Autores: Vipavc Brvar, Irena
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.11123132

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

Autores: Justin Clark-Casey; Stian Soiland-Reyes
Publicado en: ELIXIR, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7323480

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

Autores: Kleemola, Mari
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.11066716

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

Autores: Simon Saldner, Sonja Bezjak, Vasso Kalaitzi, Kondyli Dimitra, Carola Schulz, Irena Vipavc. Brvar, Patricia M Palagi
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.11220597

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

Autores: Braukmann, Ricarda
Publicado en: DANS, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7867780

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

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

Packing provenance using CPM RO-Crate profile

Autores: Rudolf Wittner, Matej Gallo, Simone Leo, Stian Soiland-Reyes
Publicado en: 2023
Editor: 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

Autores: 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
Publicado en: Edición 11, 9, 2023
Editor: Microorganisms
DOI: 10.3390/microorganisms11092251

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

Autores: Garcia Alvarez, Eva; Holub, Petr; Colussi, Ilaria; Panagiotopoulou, Maria
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13981358

Introduction to Semantic Interoperability Challenges for RIs

Autores: David, Romain; Madon, Bénédicte; Torralba, Antonio
Publicado en: Zenodo, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.8059821

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

Autores: Garcia Alvarez, Eva; Holub, Petr
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7476926

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

Autores: Nina Van Goethen; Marjan Meurisse; Javier González-Galindo; Natalia Martínez-Lizaga; Francisco Estupiñán-Romero; Enrique Bernal-Delgado
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7993140

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

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

BY-COVID D1.2: Preparedness Data Hub

Autores: Rahman, Nadim; O'Cathail, Colman; Martiny, Hannah-Marie; Ventouratou, Marianna; Waheed, Zahra; Amid, Clara; Kleemola, Mari; Neves, Aitana
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.10069940

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

Autores: Neves, Aitana; Hjerde, Erik; Ventouratou, Marianna
Publicado en: 2024
Editor: 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

Autores: 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
Publicado en: No Journal Title, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7520086

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

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

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

Autores: Ohmann, Christian; Moilanen, Katja; Kleemola, Mari; Canham, Steve; Panagiotopoulou, Maria
Publicado en: Crossref, 2023
Editor: /
DOI: 10.12688/openreseurope.16284.1

BY-COVID D6.1 Stakeholder engagement report

Autores: 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
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.12820912

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

Autores: Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas N Petersen, Oksana Lukjancenko, Frank M Aarestrup, Philip TLC Clausen, Patrick Munk
Publicado en: 2024
Editor: Bioinformatics
DOI: 10.1093/bioinformatics/btae086

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

Autores: Felder, Gerard; Contrino, Sergio; Ohmann, Christian; Panagiotopoulou, Maria; Matei, Mihaela; Kouylekov, Milen; Wolff, Russel Gene
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13981769

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

Autores: Willems, Marieke; Blomberg, Niklas; Maccallum, Peter; Tyler, Maria
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13920061

Evaluating FAIR Digital Object and Linked Data as distributed object systems

Autores: Stian Soiland-Reyes; Carole Goble; Paul Groth
Publicado en: 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
Editor: PeerJ
DOI: 10.48550/arxiv.2306.07436

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

Autores: Sousoni, Despoina; Balsyte, Erika; Harrison, Elaine; Bäckman, Ulrika; Smith, Andrew
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13889809

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

Autores: 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
Publicado en: https://hal.science/hal-04149733, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8101848

BY-COVID M7.3: Industry sector mapping report

Autores: Lauer, Katharina; Smith, Andrew; Sousoni, Despoina; Westwick, Elaine; Martin, Corinne; Alloza Anguiano, Eva; David, Romain; Blomberg, Niklas
Publicado en: By-covid, 2023
Editor: 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?

Autores: Eržen, Ivan, Fafangel, Mario, Gabrovec, Branko, Selak, Špela, Skaza, Alenka, Vrdelja, Mitja
Publicado en: Nacionalni inštitut za javno zdravje, 2022
Editor: Nacionalni inštitut za javno zdravje

Building a FAIR image data ecosystem for microscopy communities

Autores: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publicado en: Histochemistry and Cell Biology, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7788898

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

Autores: Rahman, Nadim; Zyoud, Ahman; Waheed, Zahra
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13323331

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

Autores: Van Goethem, Nina; Cavillot, Lisa
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7988733

Beyond Covid Educational Toolkit

Autores: Van Hoof, Wannes; Genten, Olivia
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.14025911

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

Autores: 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
Publicado en: Learning Health Systems, Vol 8, Iss 1, Pp n/a-n/a (2024), 2023
Editor: .
DOI: 10.5281/zenodo.5093124

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

Autores: Westwick, Elaine; Haskell, Erin; Martin, Corinne
Publicado en: BEYOND COVID, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.6884870

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

Autores: 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,
Publicado en: bioRxiv, 2023
Editor: bioRxiv
DOI: 10.1101/2023.04.19.537514

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

Autores: Willems, Marieke; Taverner, Ellie
Publicado en: BY-COVID, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7789351

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

Autores: Lavitrano, Marialuisa; Cocuzza, Clementina; Musumeci, Rosario
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13332781

The BeYond COVID project: STORIES OF SUCCESS

Autores: Harrison, Elaine; Maccallum, Peter
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.14499931

BY-COVID - D8.2 - Data Management Plan

Autores: García Álvarez, Eva; Mayrhofer, Michaela; Holub, Peter
Publicado en: BEYOND COVID, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.6884816

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

Autores: Tyler, Maria; Fernandez Hidalgo, Maria Dolores
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13985857

BY-COVID D1.1 Extended workflows

Autores: Cochrane, Guy; Amid, Clara
Publicado en: BEYOND COVID, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.7875986

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

Autores: 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
Publicado en: Scientific data, Edición 10, 2023
Editor: 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

Autores: 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
Publicado en: Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024), 2023
Editor: /
DOI: 10.21203/rs.3.rs-3159433/v1

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

Autores: Van Goethem, Nina; Bernal-Delgado, Enrique; Estupiñán-Romero, Francisco; Meurisse, Marjan
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13870075

BY-COVID deliverable 4.2: Common analysis environment

Autores: Maier, Wolfgang; Rasche, Helena; Buono, Rafael Andrade
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.12706837

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

Autores: Regina Nora Fiam, Csabai Istvan, Solymosi Norbert
Publicado en: 2023
Editor: 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

Autores: Portell-Silva, Laura
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13981571

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

Autores: Belien, Jeroen
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7982090

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

Autores: 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
Publicado en: BEYOND COVID, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7129553

The ODISSEI Portal: collecting metadata from Dutch data providers

Autores: Maineri, Angelica Maria
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7970500

Recording provenance of workflow runs with RO-Crate

Autores: 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
Publicado en: 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
Editor: /
DOI: 10.48550/arxiv.2312.07852

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

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

Open data to support European pandemic preparedness.

Autores: 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
Publicado en: BY-COVID, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7940608

BY-COVID D6.2 Training efforts report

Autores: Palagi, Patricia; Rahman, Nadim; Kleemola, Mari; Kalaitzi, Vasso; Saldner, Simon; Rasche, Helena; Kemmer, Isabel Marinna; Morgan, Sarah; Brvar, Irena Vipavc
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13349254

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

Autores: Maccallum, Peter; Hermjakob, Henning; Harrison, Elaine; Tseng, Yun-Yun
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.14001994

BY-COVID D4.1 Infectious Diseases Toolkit

Autores: Peterson, Hedi; Buono, Rafael Andrade; Portell Silva, Laura; Palagi, Patricia; Hughes, Liane; Droesbeke, Bert
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13909280

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

Autores: Alessia Catalano, Domenico Iacopetta, Jessica ceramella, Michele Pellegrino, Federica Giuzio, Maria Marra, Camillo Rosano, Carmela Saturnino, Maria Stefania Sinicropi, Stefano Aquaro
Publicado en: 2023
Editor: 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

Autores: Canham, Steve; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria
Publicado en: BEYOND COVID, 2022
Editor: Zenodo
DOI: 10.5281/zenodo.7064624

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

Autores: Ostaszewski, Marek; Messina, Francesco; Mathur, Aastha; Kemmer, Isabel; Gribbon, Philip; Stubbs, Andrew; Rasche, Helena; Portell, Laura; Ene, Erdina; Hermjakob, Henning
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13330037

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

Autores: Cesare Ernesto Maria Gruber, Fabio Giovanni Tucci, Martina Rueca, Valentina Mazzotta, Giulia Gramigna et al
Publicado en: BIOMOLECULES, Edición 13,10, 2023
Editor: Biomolecules
DOI: 10.3390/biom13101538

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

Autores: 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
Publicado en: BMC medical research methodology, Vol. 23, no.1, p. 248 [1-15] (2023), 2023
Editor: -
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

Autores: Christian Ohmann, Steve Canham, Kurt Majcen, Vittorio Meloni, Luca Pireddu, Alessandr Sulis, giovanni Delussu, Francesa Frexia, Petr Holub
Publicado en: 2024
Editor: European Commision

Building an interoperable Genomic Data Infrastructure

Autores: Coppens, Frederik
Publicado en: 2022
Editor: Zenodo
DOI: 10.5281/zenodo.6604464

BY-COVID D3.3.2 COVID-19 Data Portal

Autores: 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
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.13332975

BY-COVID D4.3 Provenance model for infectious diseases

Autores: Wittner, Rudolf; Soiland-Reyes, Stian; Leo, Simone; Meurisse, Marjan; Hermjakob, Henning
Publicado en: 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
Editor: Zenodo
DOI: 10.5281/zenodo.10927253

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

Autores: Estupiñán-Romero, Francisco; Launa-Garcés, Ramón; Van Dam, Iris; Cosgrove, Shona; Van Goethem, Nina; Bernal-Delgado, Enrique
Publicado en: Edición BEYOND COVID, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7944195

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

Autores: Rambla, Jordi; Cortada, Aina Jené; Curwin, Amy
Publicado en: 2024
Editor: 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

Autores: 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
Publicado en: 2024
Editor: Virus Research
DOI: 10.1016/j.virusres.2024.199356

BY-COVID - D8.1 - Project Management Handbook

Autores: Arenas Marquez, Juan; Troncoso Quilaqueo, Andrea
Publicado en: BEYOND COVID, 2021
Editor: Zenodo
DOI: 10.5281/zenodo.6884734

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

Autores: Katharina Lauer, Romain David, Jonathan Ewbank, Nina Van Goethem, Elaine Harrison,
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.10204209

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

Autores: Enrique Bernal-Delgado; Van Goethem, Nina
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.12636106

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

Autores: 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
Publicado en: BEYOND COVID, 2022
Editor: 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

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

The European Nucleotide Archive in 2023

Autores: David Yuan, Alisha Ahamed, Josephine Burgin, Carla Cummins, Rajkumar Devraj, Khadim Gueye, Dipayan gupta, Vikas Gupta, et al
Publicado en: 2024
Editor: Nucleic Acids Research
DOI: 10.1093/nar/gkad1067

BioHackEU22 Project 22: Plant data exchange and standard interoperability

Autores: Arend, Daniel, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, et al.
Publicado en: BioHackrXiv Preprints, 2022
Editor: 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

Autores: 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
Publicado en: 2023
Editor: 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

Autores: Van Goethem, Nina; Meurisse, Marjan; Estupiñán Romero, Francisco; Bernal-Delgado, Enrique; Saldner, Simon; Kalaitzi, Vasso
Publicado en: 2024
Editor: Zenodo
DOI: 10.5281/zenodo.12771703

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

Autores: Natalia Martínez-Lizaga; Marjan Meurisse; Francisco Estupiñan-Romero; Nina Van Goethem; Enrique Bernal-Delgado
Publicado en: BY COVID, 2023
Editor: Zenodo
DOI: 10.5281/zenodo.7625784

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

Autores: Markus Plass, Rudolf Wittner, Petr Holub, Francesca Frexia, Cecilia Mascia, Matej Gallo, Heimo Müller, Jörg Geiger
Publicado en: 2023
Editor: New Biotechnology
DOI: 10.1016/j.nbt.2023.09.006

Building a FAIR image data ecosystem for microscopy communities

Autores: Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Publicado en: Histochemestry and Cell Biology, Edición 160, 2023, Página(s) 199-209
Editor: Zenodo
DOI: 10.5281/zenodo.7788899

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

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

Autores: 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
Publicado en: bioRxiv, 2022, ISSN 2692-8205
Editor: 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

Autores: 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
Publicado en: Viruses, Edición 15,11, 2023, ISSN 1999-4915
Editor: 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

Autores: István Csabai, Krisztián Papp, Dávid Visontai et al.
Publicado en: Research Square, Edición V1, 2021, ISSN 2693-5015
Editor: Research Square
DOI: 10.21203/rs.3.rs-1177047/v1

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

Autores: Anikó Mentes, Krisztián Papp, Dávid Visontai, József Stéger, VEO Technical Working Group, István Csabai, Anna Medgyes-Horváth & Orsolya Anna Pipek
Publicado en: Scientific Reports, Edición 12, 2022, ISSN 2045-2322
Editor: Springer Nature
DOI: 10.1038/s41598-022-21953-3

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

Autores: Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
Publicado en: Bioinformatics Advances, Edición 3 (1), 2023, ISSN 2635-0041
Editor: Oxford University Press
DOI: 10.1093/bioadv/vbad045

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

Autores: Istvan Csabai, Norbert Solymosi
Publicado en: Research Square, 2022, ISSN 2693-5015
Editor: Research Square
DOI: 10.21203/rs.3.rs-1330800/v1

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

Autores: Fábio Madeira, Matt Pearce, Adrian R N Tivey, Prasad Basutkar, Joon Lee, Ossama Edbali, Nandana Madhusoodanan, Anton Kolesnikov, Rodrigo Lopez
Publicado en: Nucleic Acids Research, Edición 50, 2022, ISSN 1362-4962
Editor: Oxford Academic
DOI: 10.1093/nar/gkac240

Pharmacological profiles of neglected tropical disease drugs

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

Updating Linked Data practices for FAIR Digital Object principles

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

Viruses

Autores: 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
Publicado en: Viruses, 2024, ISSN 1999-4915
Editor: MDPI
DOI: 10.3390/v16030430

Virus Research

Autores: 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
Publicado en: Virus Research, 2024, ISSN 0168-1702
Editor: 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

Autores: 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
Publicado en: Antibiotics, 2024, ISSN 2079-6382
Editor: MDPI AG
DOI: 10.3390/antibiotics13060561

Lightweight Distributed Provenance Model for Complex Real–world Environments

Autores: Wittner, R., Mascia, C., Gallo, M. et al.
Publicado en: Scientific Data, 2022, ISSN 2052-4463
Editor: Springer Nature
DOI: 10.1038/s41597-022-01537-6

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

Autores: 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.
Publicado en: Learning Health Systems, 2023, ISSN 2379-6146
Editor: Wiley
DOI: 10.1002/lrh2.10365

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

Autores: 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
Publicado en: Molecular Biology and Evolution, Edición 39 (4), 2022, ISSN 1537-1719
Editor: 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

Autores: Axel Abelein, Simone Ciofi-Baffoni, Cecilia Mörman, Rakesh Kumar, Andrea Giachetti, Mario Piccioli, and Henrik Biverstål
Publicado en: JACS Au, Edición 2, 11, 2022, ISSN 2691-3704
Editor: American Chemical Society
DOI: 10.1021/jacsau.2c00438

Angewandte Chemie - International Edition

Autores: Berg, Hannes et al.
Publicado en: Angew Chem Int Ed Engl., Edición 63, 26, 2024, ISSN 1433-7851
Editor: Wiley-VCH
DOI: 10.1002/anie.202205858

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

Autores: Chiara, M., Horner, D.S., Ferrandi, E. et al.
Publicado en: Communications biology, 2023, ISSN 2399-3642
Editor: Springer Nature
DOI: 10.1038/s42003-023-04784-4

RO-Crates Meets FAIR Digital Objects

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

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

Autores: 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
Publicado en: Scientific Reports, 2022, ISSN 1476-4687
Editor: Scientific Reports
DOI: 10.1038/s41598-022-21953-3

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

Autores: Regina Nóra Fiam; Csabai István; Solymosi Norbert
Publicado en: Briefings in Bioinformatics, 2023, ISSN 1477-4054
Editor: Oxford University Press
DOI: 10.1093/bib/bbae296

Ten Simple Rules for making a software tool workflow-ready

Autores: Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al.
Publicado en: PLoS Comput Biol, 2022, ISSN 1553-7358
Editor: 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.

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

Viruses

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

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

Autores: Stian Soiland-Reyes; Leyla Jael Castro; Rohitha Ravinder; Claus Weiland; Jonas Grieb; Alexander Rogers; Christophe Blanchi; Herbert Van de Sompel
Publicado en: 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
Editor: BioHackrXiv
DOI: 10.37044/osf.io/gmk2h

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

Autores: Van Hoof, Wannes; Genten, Olivia; Kalaitzi, Vasso; Martin, Corinne
Publicado en: 2023
Editor: Zenodo
DOI: 10.5281/zenodo.8405780

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

Autores: 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
Publicado en: 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
Editor: Zenodo
DOI: 10.5281/zenodo.8386828

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