Beyond COVID

Research InfrastructuresHORIZON-RIAID: 101046203
EC Contribution
€120,000
Consortium Size
54 orgs
Start Year
2021
Summary

Beyond-COVID (BY-COVID) aims to provide comprehensive open data on SARS-CoV-2, and other infectious diseases across scientific, medical, public health and policy domains. The project will have a strong emphasis on mobilising raw viral sequences, helping to identify and monitor the spread of SARS-CoV-2 variants. It will further accelerate access to and linking of data and metadata on SARS-CoV-2 and COVID-19, enable federated data analysis conform with data protection regulations, and harmonisation and management of meta-data and sample- identifiers, as well as long-term cataloguing to ensure interoperability of national and global efforts.BY-COVID will align with the One-Health approach building on the latest technological advances, exploiting and contributing to the European Open Science Cloud capabilities for data access and federation as well as relevant standards and policies for managing, sharing and reusing research data, and work closely with the proposal funded through the sibling-topic from the emergency call (HORIZON-INFRA-2021-EMERGENCY-02). BY-COVID will integrate established national and European infrastructures including ELIXIR, BBMRI, ECRIN, PHIRI and CESSDA. It will build on existing efforts, such as the COVID-19 Data Platform and the Versatile emerging infectious disease observatory project (VEO), thereby maximising efficiency. Synergies with the European Health Data Space will be developed.BY-COVID is a truly interdisciplinary (55 partners from 19 countries) project bringing together stakeholders from the biomedical field, hospitals, public health, social sciences and humanities in an unprecedented and unique effort and will increase European readiness for future pandemics enhance genomic surveillance and rapid-response capabilities. The outputs of the project will allow scientists across multiple domains, including SMEs and industry, to access a range of data that will generate new knowledge on infectious disease.

Consortium (54)

🇩🇪 EUROPEAN MOLECULAR BIOLOGY LABORATORYDE
coordinator
🇳🇱 ACADEMISCH ZIEKENHUIS GRONINGENNL
partner
AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
partner
🇩🇪 ALBERT-LUDWIGS-UNIVERSITAET FREIBURGDE
partner
🇪🇸 BARCELONA SUPERCOMPUTING CENTER CENTRO NACIONAL DE SUPERCOMPUTACIONES
partner
🇦🇹 BIOBANKS AND BIOMOLECULAR RESOURCES RESEARCH INFRASTRUCTURE CONSORTIUM (BBMRI-ERIC)AT
partner
🇮🇹 CENTRO DI RICERCA, SVILUPPO E STUDI SUPERIORI IN SARDEGNA SOCIETÀ A RESPONSABILITÀ LIMITATAIT
partner
🇳🇴 CESSDA ERICNO
partner
CONSIGLIO NAZIONALE DELLE RICERCHE
partner
🇮🇹 CONSORZIO INTERUNIVERSITARIO RISONANZE MAGNETICHE DI METALLO PROTEINEIT
partner
DANMARKS TEKNISKE UNIVERSITET
partner
🇳🇱 EATRIS ERICNL
partner
🇫🇷 ECRIN EUROPEAN CLINICAL RESEARCH INFRASTRUCTURE NETWORKFR
partner
🇩🇪 EMPIRICA GESELLSCHAFT FUR KOMMUNIKATIONS UND TECHNOLOGIEFORSCHUNG MBHDE
partner
🇭🇺 EOTVOS LORAND TUDOMANYEGYETEMHU
partner
🇳🇱 ERASMUS UNIVERSITAIR MEDISCH CENTRUM ROTTERDAMNL
partner
🇬🇷 ETHNIKO KENTRO KOINONIKON EREVNONGR
partner
🇫🇮 EURO-BIOIMAGING ERICFI
partner
🇩🇪 EUROPEAN INFRASTRUCTURE OF OPEN SCREENING PLATFORMS FOR CHEMICAL BIOLOGY EUROPEAN RESEARCH INFRASTUCTURE CONSORTIUM (EU-OPENSCREEN ERIC)DE
partner
🇧🇪 EUROPEAN RESEARCH INFRASTRUCTURE ON HIGHLY PATHOGENIC AGENTSBE
partner
🇮🇹 EUROPEAN UNIVERSITY INSTITUTEIT
partner
🇩🇪 FRAUNHOFER GESELLSCHAFT ZUR FORDERUNG DER ANGEWANDTEN FORSCHUNG EVDE
partner
🇪🇸 FUNDACIO CENTRE DE REGULACIO GENOMICAES
partner
🇦🇹 GESUNDHEIT OSTERREICH GMBHAT
partner
🇩🇪 INFRAFRONTIER ERICDE
partner
🇨🇿 INSTITUTE OF SOCIOLOGY OF THE ACADEMY OF SCIENCES OF THE CZECH REPUBLIC PUBLIC RESEARCH INSTITUTIONCZ
partner
🇪🇸 INSTITUTO ARAGONES DE CIENCIAS DE LA SALUDES
partner
🇬🇧 INSTRUCT-ERICGB
partner
🇮🇹 IRCCS OSPEDALE POLICLINICO SAN MARTINOIT
partner
🇮🇹 ISTITUTO NAZIONALE PER LE MALATTIE INFETTIVE LAZZARO SPALLANZANI-ISTITUTO DI RICOVERO E CURA A CARATTERE SCIENTIFICOIT
partner
🇮🇹 ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLA LOMBARDIA E DELL'EMILIA ROMAGNA BRUNO UBERTINIIT
partner
🇮🇹 ISTITUTO ZOOPROFILATTICO SPERIMENTALE DELLE VENEZIEIT
partner
🇳🇱 KONINKLIJKE NEDERLANDSE AKADEMIE VAN WETENSCHAPPEN - KNAWNL
partner
🇰🇷 KOREA RESEARCH INSTITUTE OF STANDARDS AND SCIENCEKR
partner
🇨🇿 MASARYKOVA UNIVERZITACZ
partner
🇳🇱 RIJKSINSTITUUT VOOR VOLKSGEZONDHEID EN MILIEUNL
partner
🇧🇪 SCIENSANOBE
partner
🇨🇭 SIB SWISS INSTITUTE OF BIOINFORMATICSCH
partner
🇳🇱 STICHTING AMSTERDAM UMCNL
partner
🇳🇱 STICHTING LYGATURENL
partner
🇫🇮 TAMPEREEN KORKEAKOULUSAATIO SRFI
partner
🇪🇪 TARTU ULIKOOLEE
partner
🇫🇮 TERVEYDEN JA HYVINVOINNIN LAITOSFI
partner
🇬🇧 THE CHANCELLOR, MASTERS AND SCHOLARS OF THE UNIVERSITY OF OXFORDGB
partner
🇬🇧 THE UNIVERSITY OF MANCHESTERGB
partner
🇬🇧 THE UNIVERSITY OF NOTTINGHAMGB
partner
🇮🇹 UNIVERSITA' DEGLI STUDI DI MILANO-BICOCCAIT
partner
🇱🇺 UNIVERSITE DU LUXEMBOURGLU
partner
🇳🇴 UNIVERSITETET I OSLONO
partner
🇳🇴 UNIVERSITETET I TROMSOE - NORGES ARKTISKE UNIVERSITETNO
partner
🇸🇮 UNIVERZA V LJUBLJANISI
partner
🇨🇿 UNIVERZITA PALACKEHO V OLOMOUCICZ
partner
🇸🇪 UPPSALA UNIVERSITETSE
partner
🇧🇪 VIB VZWBE
partner

Project Results (142)

Source: CORDIS, the EU research results database.

Publications (111)
An assessment of the informative value of data sharing statements in clinical trial registries
BMC Medical Research Methodology, Vol 24, Iss 1, Pp 1-11 (2024)· 2024DOI
Christian Ohmann; Maria Panagiotopoulou; Steve Canham; Gerd Felder; Pablo Emilio Verde
Beyond Covid Educational Toolkit
· 2024DOI
Van Hoof, Wannes; Genten, Olivia
BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment - Data Management Plan
· 2024DOI
Enrique Bernal-Delgado; Van Goethem, Nina
BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Local outputs and comparative analysis
· 2024DOI
Meurisse, Marjan; Estupiñán-Romero, Francisco; Van Goethem, Nina; Perola, Markus; Paajanen, Teemu; González-Galindo, Javier; Bernal-Delgado, Enrique
BY-COVID D1.3. Tracking and open analytics tools
· 2024DOI
Rahman, Nadim; Zyoud, Ahman; Waheed, Zahra
BY-COVID D1.4 The repurposing of 2 national SARS-CoV-2 data portals towards national pathogen portals
· 2024DOI
Neves, Aitana; Hjerde, Erik; Ventouratou, Marianna
BY-COVID D2.3 Enabling data discovery at source using beacon-like mechanisms
· 2024DOI
Rambla, Jordi; Cortada, Aina Jené; Curwin, Amy
BY-COVID D2.4 Report on data sources discovery and integration for enabling data use and re-use in response to future outbreaks
· 2024DOI
Portell-Silva, Laura
BY-COVID D3.3.2 COVID-19 Data Portal
· 2024DOI
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
BY-COVID D4.1 Infectious Diseases Toolkit
· 2024DOI
Peterson, Hedi; Buono, Rafael Andrade; Portell Silva, Laura; Palagi, Patricia; Hughes, Liane; Droesbeke, Bert
BY-COVID D4.3 Provenance model for infectious diseases
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· 2024DOI
Wittner, Rudolf; Soiland-Reyes, Stian; Leo, Simone; Meurisse, Marjan; Hermjakob, Henning
BY-COVID D5.1 Enriched report viral variants and health outcomes
· 2024DOI
Van Goethem, Nina; Bernal-Delgado, Enrique; Estupiñán-Romero, Francisco; Meurisse, Marjan
BY-COVID D5.2 Secondary use of vaccine trial data and biosamples
· 2024DOI
Felder, Gerard; Contrino, Sergio; Ohmann, Christian; Panagiotopoulou, Maria; Matei, Mihaela; Kouylekov, Milen; Wolff, Russel Gene
BY-COVID D5.3a Mechanistic analyses via the COVID-19 Disease Map
· 2024DOI
Ostaszewski, Marek; Messina, Francesco; Mathur, Aastha; Kemmer, Isabel; Gribbon, Philip; Stubbs, Andrew; Rasche, Helena; Portell, Laura; Ene, Erdina; Hermjakob, Henning
BY-COVID D5.3b Hot Spot detection through wastewater surveillance and samples data collection
· 2024DOI
Lavitrano, Marialuisa; Cocuzza, Clementina; Musumeci, Rosario
BY-COVID D6.1 Stakeholder engagement report
· 2024DOI
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
BY-COVID D6.2 Training efforts report
· 2024DOI
Palagi, Patricia; Rahman, Nadim; Kleemola, Mari; Kalaitzi, Vasso; Saldner, Simon; Rasche, Helena; Kemmer, Isabel Marinna; Morgan, Sarah; Brvar, Irena Vipavc
BY-COVID D7.2 - Report on industry value of infectious disease data
· 2024DOI
Sousoni, Despoina; Balsyte, Erika; Harrison, Elaine; Bäckman, Ulrika; Smith, Andrew
BY-COVID D8.1.3 Project Handbook initial release and periodic updates
· 2024DOI
Tyler, Maria; Fernandez Hidalgo, Maria Dolores
BY-COVID D8.2.3 Project Data Management Plan initial release and periodic updates
· 2024DOI
Garcia Alvarez, Eva; Holub, Petr; Colussi, Ilaria; Panagiotopoulou, Maria
BY-COVID D8.3 BY-COVID Long Term Sustainability Plan
· 2024DOI
Willems, Marieke; Blomberg, Niklas; Maccallum, Peter; Tyler, Maria
BY-COVID D8.5 Policy Brief II: Research data infrastructure for sustainable global pandemic preparedness
· 2024DOI
Maccallum, Peter; Hermjakob, Henning; Harrison, Elaine; Tseng, Yun-Yun
BY-COVID deliverable 4.2: Common analysis environment
· 2024DOI
Maier, Wolfgang; Rasche, Helena; Buono, Rafael Andrade
Data sharing and reuse under GDPR - BY-COVID Fest workshop report
· 2024DOI
Simon Saldner, Sonja Bezjak, Vasso Kalaitzi, Kondyli Dimitra, Carola Schulz, Irena Vipavc. Brvar, Patricia M Palagi
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches
Frontiers in Immunology· 2024DOI
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
Euro-BioImaging's Template for Research Data Management Plans
· 2024DOI
Kemmer, Isabel; Euro-BioImaging ERIC
Evaluating FAIR Digital Object and Linked Data as distributed object systems
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· 2024DOI
Stian Soiland-Reyes; Carole Goble; Paul Groth
How to make your sensitive data FAIR: use case in social sciences
· 2024DOI
Kleemola, Mari
Linking the ECRIN Metadata Repository with the BBMRI-ERIC Directory to connect clinical studies with related biobanks and collections
· 2024
Christian Ohmann, Steve Canham, Kurt Majcen, Vittorio Meloni, Luca Pireddu, Alessandr Sulis, giovanni Delussu, Francesa Frexia, Petr Holub
Molecular Characterization of Multidrug-Resistant and Hypervirulent New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae in Lazio, Italy: A Five-Year Retrospective Study
Antibiotics· 2024DOI
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
Pharmacological profiles of neglected tropical disease drugs
Artificial Intelligence in the Life Sciences· 2024DOI
Alessandro Greco; Reagon Karki; Yojana Gadiya; Clara Deecke; Andrea Zaliani; Sheraz Gul
Sanitary Waters: Is It Worth Looking for Mycobacteria?
Microorganisms· 2024DOI
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
Screening of Klebsiella pneumoniae subsp. pneumoniae Strains with Multi-Drug Resistance and Virulence Profiles Isolated from an Italian Hospital between 2020 and 2023
Antibiotics· 2024DOI
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
The BeYond COVID project: STORIES OF SUCCESS
· 2024DOI
Harrison, Elaine; Maccallum, Peter
Towards a common standard for data and specimen provenance in life sciences
Learning Health Systems· 2024DOI
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.
Virus Research
Virus Research· 2024DOI
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
Viruses
Viruses· 2024DOI
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
"EOSC-Future Test Science Project ""META-COVID"": Final report for CESSDA – ECRIN use case"
· 2023DOI
Ohmann, Christian; Panagiotopoulou, Maria; Moilanen, Katja; Kleemola, Mari
"Preprint: ""Be Sustainable"", Recommendations for FAIR Resources in Life Sciences research: EOSC-Life's Lessons"
Zenodo· 2023DOI
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
Beyond COVID - how the BY-COVID project is increasing European pandemic preparedness
· 2023DOI
Katharina Lauer, Romain David, Jonathan Ewbank, Nina Van Goethem, Elaine Harrison,
Building a FAIR image data ecosystem for microscopy communities
Histochemistry and Cell Biology· 2023DOI
Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
BY-COVID - WP5 - Baseline Use Case: Integration of socioeconomic data in observational studies using a prototyped workflow standard to federated population health research
· 2023DOI
Van Goethem, Nina; Meurisse, Marjan; Estupiñán Romero, Francisco; Bernal-Delgado, Enrique; Saldner, Simon; Kalaitzi, Vasso
BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment preliminary outputs from Aragon, Spain
· 2023DOI
Estupiñán-Romero, Francisco; González-Galindo, Javier; Meurisse, Marjan; Martínez-Lizaga, Natalia; Royo-Sierra, Santiago; Van Goethem, Nina; Bernal-Delgado, Enrique
BY-COVID D1.2: Preparedness Data Hub
· 2023DOI
Rahman, Nadim; O'Cathail, Colman; Martiny, Hannah-Marie; Ventouratou, Marianna; Waheed, Zahra; Amid, Clara; Kleemola, Mari; Neves, Aitana
BY-COVID D2.2: Data Access and Transfer across research domains and jurisdictions
https://hal.science/hal-04149733· 2023DOI
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
BY-COVID D3.3.1: COVID-19 Data Portal
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· 2023DOI
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
BY-COVID D7.3: Report on public engagement activities
· 2023DOI
Van Hoof, Wannes; Genten, Olivia; Kalaitzi, Vasso; Martin, Corinne
BY-COVID Deliverable 8.1.2 Project Handbook initial release and periodic updates
BY-COVID· 2023DOI
Willems, Marieke; Taverner, Ellie
BY-COVID M7.3: Industry sector mapping report
By-covid· 2023DOI
Lauer, Katharina; Smith, Andrew; Sousoni, Despoina; Westwick, Elaine; Martin, Corinne; Alloza Anguiano, Eva; David, Romain; Blomberg, Niklas
BY-COVID Milestone 2.2 Mechanism for data access and use of routine real-world data
· 2023DOI
Estupiñán-Romero, Francisco; Launa-Garcés, Ramón; Van Dam, Iris; Cosgrove, Shona; Van Goethem, Nina; Bernal-Delgado, Enrique
BY-COVID Spring 23 Use Cases Workshop: Integration of socioeconomic data in observational studies on vaccine effectiveness
· 2023DOI
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
Continuously evolving demonstrator - Baseline use case: Prototyping a workflow that is standard to population health research
· 2023DOI
Nina Van Goethen; Marjan Meurisse; Javier González-Galindo; Natalia Martínez-Lizaga; Francisco Estupiñán-Romero; Enrique Bernal-Delgado
Data landscape for infectious diseases surveillance in Belgium and use of socio-economic indicators
· 2023DOI
Van Goethem, Nina; Cavillot, Lisa
ECRIN – CESSDA strategies for cross metadata mappings in selected areas between life sciences and social sciences and humanities
Crossref· 2023DOI
Ohmann, Christian; Moilanen, Katja; Kleemola, Mari; Canham, Steve; Panagiotopoulou, Maria
Epidemiological and Molecular Investigation of the Heater–Cooler Unit (HCU)-Related Outbreak of Invasive Mycobacterium chimaera Infection Occurred in Italy
Microorganisms· 2023DOI
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
Federated causal inference based on real-world observational data sources: application to a SARS-CoV-2 vaccine effectiveness assessment
BMC medical research methodology, Vol. 23, no.1, p. 248 [1-15] (2023)· 2023DOI
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
Hands on social sciences data anonymization exercise
· 2023DOI
Vipavc Brvar, Irena
HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2
Communications biology· 2023DOI
Chiara, M., Horner, D.S., Ferrandi, E. et al.
Health-RI COVID19 project Experiences and bottlenecks re: SSH data
· 2023DOI
Belien, Jeroen
Improving Galaxy provenance export using RO-Crate
GALAXY TRAINING· 2023DOI
Paul De Geest; Frederik Coppens; Ignacio Eguinoa; Stian Soiland-Reyes; Simone Leo
Instruct-ERIC Annual Report 2022
· 2023DOI
Instruct-ERIC
Instruct-ERIC Annual Report 2023
· 2023DOI
Instruct-ERIC
Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate
F1000RESEARCH· 2023DOI
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
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses
bioRxiv· 2023DOI
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,
Mpox Knowledge Graph: A comprehensive representation embedding chemical entities and associated biology of Mpox
Bioinformatics Advances· 2023DOI
Reagon Karki, Yojana Gadiya, Andrea Zaliani, Philip Gribbon
Open data to support European pandemic preparedness.
· 2023DOI
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
Packing provenance using CPM RO-Crate profile
· 2023DOI
Rudolf Wittner, Matej Gallo, Simone Leo, Stian Soiland-Reyes
Provenance of specimen and data – A prerequisite for AI development in computational pathology
New Biotechnology· 2023DOI
Plass, Markus; Wittner, Rudolf; Holub, Petr; Frexia, Francesca; Mascia, Cecilia; Gallo, Matej; Müller, Heimo; Geiger, Jörg
Recording provenance of workflow runs with RO-Crate
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· 2023DOI
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
RO-Crates Meets FAIR Digital Objects
Proceedings of the Conference on Research Data Infrastructure· 2023DOI
Castro, Leyla Jael; Soiland-Reyes, Stian; Rebholz-Schuhmann, Dietrich
Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples
Nature Communications, Vol 15, Iss 1, Pp 1-13 (2024)· 2023DOI
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
The DANS Data Station Social Sciences & Humanities - Enabling FAIR data in the Dutch SSH community
DANS· 2023DOI
Braukmann, Ricarda
The FAIR Cookbook - the essential resource for and by FAIR doers
Scientific data· 2023DOI
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
The ODISSEI Portal: collecting metadata from Dutch data providers
· 2023DOI
Maineri, Angelica Maria
Toward a common standard for data and specimen provenance in life sciences
Learning Health Systems, Vol 8, Iss 1, Pp n/a-n/a (2024)· 2023DOI
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
Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness
· 2023DOI
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
Viruses
Viruses· 2023DOI
Alessia Catalano; Domenico Iacopetta; Jessica Ceramella; Michele Pellegrino; Federica Giuzio; Maria Marra; Camillo Rosano; Carmela Saturnino; Maria Stefania Sinicropi; Stefano Aquaro
BioHackEU22 Project 22: Plant data exchange and standard interoperability
BioHackrXiv Preprints· 2022DOI
Arend, Daniel, Sebastian Beier, laurent bouri, Marco Brandizi, Donald Hobern, Erwan Le Floch, Timo Mühlhaus, et al.
Building an interoperable Genomic Data Infrastructure
· 2022DOI
Coppens, Frederik
BY-COVID - D3.1 - Metadata standards. Documentation on metadata standards for inclusion of resources in data portal
BEYOND COVID· 2022DOI
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
BY-COVID - D7.1 - Communication, Dissemination and Exploitation Strategy
BEYOND COVID· 2022DOI
Westwick, Elaine; Haskell, Erin; Martin, Corinne
BY-COVID D3.2: Implementation of cloud-based, high performance, scalable indexing system.
BEYOND COVID· 2022DOI
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
BY-COVID D8.2.2 Project Data Management Plan initial release and periodic updates M15
· 2022DOI
Garcia Alvarez, Eva; Holub, Petr
BY-COVID- D2.1 - Initial data and metadata harmonisation at domain level to enable fast responses to COVID-19
BEYOND COVID· 2022DOI
Giles, Tom; Quinlan, Phil; Belien, Jeroen; Lischke, Julia; Portell-Silva, Laura; Capella-Gutierrez, Salvador; Karki, Reagon; Kalaitzi, Vasso; Bernal-Delgado, Enrique; Keppler, Antje
Community-driven governance of FAIRness assessment: an open issue, an open discussion
Open Research Europe· 2022DOI
Mark D. Wilkinson; Susanna-Assunta Sansone; Eva Méndez; Romain David; Richard Dennis; David Hecker; Mari Kleemola; Carlo Lacagnina; Anastasija Nikiforova; Leyla Jael Castro
Comprehensive Fragment Screening of the SARS-CoV-2 Proteome Explores Novel Chemical Space for Drug Development
Angewandte Chemie. International Edition, 61 (46)· 2022DOI
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.
Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting
MANCHESTER 1824· 2022DOI
Stian Soiland-Reyes; Peter Sefton; Leyla Jael Castro; Frederik Coppens; Daniel Garijo; Simone Leo; Marc Portier; Paul Groth; Carole Goble
Enhancing RDM in Galaxy by integrating RO-Crate
Research Ideas and Outcomes· 2022DOI
Paul De Geest; Frederik Coppens; Stian Soiland-Reyes; Ignacio Eguinoa; Simone Leo
Galaxy Training: A Powerful Framework for Teaching!
PLOS Computational Biology· 2022DOI
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
Host genomes for the unique SARS-CoV-2 variant leaked into Antarctic soil metagenomic sequencing data
Research Square· 2022DOI
Istvan Csabai, Norbert Solymosi
Identification of COVID-19 clinical studies intending to share individual participant data for secondary use: Protocol for a pilot study
BEYOND COVID· 2022DOI
Canham, Steve; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria
Identification of mutations in SARS-CoV-2 PCR primer regions
Scientific Reports· 2022DOI
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
Introduction to Semantic Interoperability Challenges for RIs
Zenodo· 2022DOI
David, Romain; Madon, Bénédicte; Torralba, Antonio
Lightweight Distributed Provenance Model for Complex Real–world Environments
Scientific Data· 2022DOI
Wittner, R., Mascia, C., Gallo, M. et al.
Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories
ELIXIR· 2022DOI
Justin Clark-Casey; Stian Soiland-Reyes
Packaging research artefacts with RO-Crate
Data Science· 2022DOI
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
RO-Crate: packaging metadata love notes into FAIR Digital Objects
ZENODO· 2022DOI
Goble, Carole; Soiland-Reyes, Stian
Semi-automatic mapping of external scientific databases into the FAIRsharing platform
FAIRsharing· 2022DOI
Ramon; Delphine; Allyson; Milo; Susanna-Assunta
Sustainability of FAIR Life Science Resources and Projects: Lessons Learned from EOSC-Life Research Infrastructures
Zenodo· 2022DOI
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
Ten Simple Rules for making a software tool workflow-ready
PLoS Comput Biol· 2022DOI
Brack P, Crowther P, Soiland-Reyes S, Owen S, Lowe D, Williams AR, et al.
The European Nucleotide Archive in 2022
Nucleic Acids Research· 2022DOI
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
Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance
bioRxiv· 2022DOI
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
Updating Linked Data practices for FAIR Digital Object principles
Research Ideas and Outcomes· 2022DOI
Soiland-Reyes S, Castro LJ, Garijo D, Portier M, Goble C, Groth P
Updating Linked Data practices for FAIR Digital Object principles
RIO· 2022DOI
Stian Soiland-Reyes; Leyla Jael Castro; Daniel Garijo; Marc Portier; Carole Goble; Paul Groth
Zakaj je arhiviranje podatkov v času covid-19 pomembno? Why is data archiving important in the covid-19 era?
Nacionalni inštitut za javno zdravje· 2022
Eržen, Ivan, Fafangel, Mario, Gabrovec, Branko, Selak, Špela, Skaza, Alenka, Vrdelja, Mitja
BY-COVID - D8.1 - Project Management Handbook
BEYOND COVID· 2021DOI
Arenas Marquez, Juan; Troncoso Quilaqueo, Andrea
BY-COVID - D8.2 - Data Management Plan
· 2021DOI
García Álvarez, Eva; Mayrhofer, Michaela; Holub, Peter
BY-COVID - WP5 - Baseline Use Case: COVID-19 vaccine effectiveness assessment - Study protocol
· 2021DOI
Meurisse, Marjan; Van Goethem, Nina; Estupiñán-Romero, Francisco; González-Galindo, Javier; Royo-Sierra, Santiago; Martínez Lizaga, Natalia; Bernal-Delgado, Enrique
BY-COVID D1.1 Extended workflows
BEYOND COVID· 2021DOI
Cochrane, Guy; Amid, Clara
Unique SARS-CoV-2 variant found in public sequence data of Antarctic soil samples collected in 2018-2019
Research Square· 2021DOI
István Csabai, Krisztián Papp, Dávid Visontai et al.
Instruct-ERIC Annual Report 2021
· 2020DOI
Instruct-ERIC
Deliverables (30)
Documents, reports
Documents, reports
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Websites, patent fillings, videos etc.
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Other Results (1)
Periodic Reporting for period 2 - BY-COVID (Beyond COVID)