Connect and align ELIXIR Nodes to deliver sustainable FAIR life-science data management services

Risultati finali

Toolkit extension based on first wave demonstrators

Apply processes to extend the toolkit addressing additional communities

Updated ELIXIR Long-term Sustainability Plan

An overview of actions that aim to support the sustainability of bioinformatics resources across ELIXIRs Nodes

Retrospective assessment of national use-cases, identification of gaps, and recommendations for future Federated EGA roadmap

Retrospective assessment of national usecases identification of gaps and recommendations for future Federated EGA roadmap to facilitate adoption of FEGA by ELIXIR National Nodes and 1MG National Mirror Groups

Report on mobilised sequence and variation data
Project Handbook 1v0

Initial version of the Project Handbook following Open PM best practices

Categorization of the pilot projects

Description of the needs in term of DMP of the demonstrator projects and development of a projects categorization from that point of view

1st Report on delivered data management and stewardship courses

Report listing the delivered training events related to data management and stewardship encompassing both reruns of existing Node courses as well as delivering of new courses developed in Task 22

A pan-European model for coordinated data management in life sciences

Description of an operating model for coordinated Node support to international projects

Access to EU tools and project data

Systems to capture and maintain user tools and datasets internal and external to EMBLEBIs molecular data resources using the ELIXIR biotools registry and the EMBLEBI BioStudies database

Report on the remaining four DMP processes

Description on the remaining DMPs constructed taking into consideration the outcomes of the previous experiences

Phylogenetic tools and enhanced results visualisation

Improved navigation and visualisation tools for systematic processing and analysis including phylogenetic trees

Report on operational processes across the federated EGA network and data transfer with the European COVID-19 platform

This report will provide details and links to the documentation best practices and SOPs for operating EGA nodes and details of how EGA COVID19 studies can be published in the European COVID19 platform

Industry engagement wiki guide for ELIXIR Nodes

A continuously updated and communitybuilt guide for Nodes on how to engage with industry

Report on the first two DMP process

Description of the first two DMPs coconstructed with WP3 including the gap analysis

Extended toolkit

Harmonized toolkit including expansion with second wave of demonstrators

Workshop to explore and plan the inclusion of tools and data from projects that have diverted towards COVID-19 research

Workshop to explore and plan inclusion of tools and data from projects that have diverted towards COVID19 research

Document where code from the various regional/national data hubs is available; links to analysis tools made available to Data Hubs; training documentation on data submission by the platforms

Document where code from the various regionalnational data hubs is available links to analysis tools made available to Data Hubs training documentation on data submission by the platforms

Survey of business models

Survey of existing business models used to deliver national data management support with gap analysis against identified needs

Report on the dedicated training and capacity building activities

Report on the training and capacity building activities coconstructed with WP2

Report of use-cases and architecture for the EGA federation

A description of the target usecases that will be fulfilled by Federated EGA and how these are met by the proposed network architecture

COVID-19 metadata mapping model across COVID-19 studies in federated EGA

This report will provide details of the metadata mapping between the COVID19 submissions to Federated EGA nodes to enable cross cohort discovery queries and joint analysis

Report on the outreach activities and training activities produced

Overview of all data management and stewardship related training and outreach activities that have been undertaken in and for emerging ELIXIR Nodes and Communities

Report on the identified training needs and a timeline for training courses

Data Management Training roadmap with contents and timeline for DM courses to be developed in ELIXIRCONVERGE

Dissemination of the toolkit across the ERA

Training and capacity building of all stakeholders

Data access points and tools

New and enhanced data access points to SARSCoV2 data supporting such operations as full data synchronisation accessibility from external cloud compute and embedding in third party tools

Project Handbook 2v0

Update of the Project Handbook including update on the KPIs

2nd Report on delivered data management and stewardship courses

Report listing the delivered training events related to data management and stewardship encompassing both reruns of existing Node courses as well as delivering of new courses developed in Task 22

Implementation and documentation to create an operational EGA node

The report will include details of the implementation of the Local EGA node outlining the main areas of functionality and include links to public documentation necessary to create deploy and operate the instance

Project Handbook final version and lesson learnt

Final version of the Project Handbook KPIs and lesson learnt

Best practices documents on data standards
Report on KPI

Report on KPIs developed for WP5 based on demonstrator projects

Review of effectiveness of the Node Impact Assessment Toolkit

An analysis of the effectiveness of the Impact Assessment Toolkit including outcomes of its application at Nodelevel

Assembled starter toolkit

Toolkit blueprints for omics and sensitive data assembled

Best Practices, version 1

A first version of best practices for data management based upon the early use cases and initial projects

Raw sequence data processing workflow in operation

Systematic and autonomous processing and analysis of incoming data with preliminary results presentation

Report on the ready-to-use training materials for usage and rolling-out in Task 2.3

Report listing all new DM training materials that have been developed and that are findable and reusable via TeSS

ELIXIR Best Practices recommendations

Final best practice recommendations incorporating use of data brokering business models and panEuropean operations

Single entry-point portal for the toolkit for all stakeholders

Components of the toolkit integrated into the portal

Pubblicazioni

ELIXIR-CONVERGE D1.2 Survey of business models

Autori: Carraro, Marco; Tosatto, Silvio; Jareborg, Niclas; Berka, Karel; Martin, Corinne; d'Anna, Flora; Bösl, Korbinian; Jetten, Mijke; Andrews, Robert; Vergoulis, Thanasis; Arenas Marquez, Juan; Smith, Andrew; Hooft, Rob; Pižemová, Natália; Ahokas, Minna; Silva, Mário; Inno, Heleri; Wittig, Ulrike; Alper, Pinar; Ben-Avraham, Danny; Lieby, Paulette; Gu, Wei
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6344131

What does FAIR mean to you?

Autori: R.W.W. Hooft
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7323398

ELIXIR-CONVERGE D7.2 Implementation and documentation to create an operational EGA node

Autori: Rambla, Jordi; D'Altri, Teresa; Haziza, Frédéric
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4893190

ELIXIR-CONVERGE D4.3 Review of effectiveness of the Node Impact Assessment Toolkit

Autori: Martin, Corinne; De Ruyck, Kim; Portugal Melo, Ana; Stansberg, Christine; Alloza, Eva; Anton, Mihail; Balsyte, Erika; Barlow, Mary; Bruno, Chiara; Ben-Avraham, Danny; Battistella, Diana; Blomberg, Niklas; Chasapi, Anastasia; Cook, Martin; Dangles, Marie; De Freitas, Mariana; Delva, Emily; Dubar, Elsa; De Leo, Francesca; Farrell, Gavin; Ferk, Polonca; van Gelder, Celia; Gurwitz, Kim; Harrison, Elai
Pubblicato in: 2023
Editore: Zedodo
DOI: 10.5281/zenodo.8169303

ELIXIR-CONVERGE D9.2 Document where code from the various regional/national data hubs is available; training documentation on data submission by the platforms - relates to tasks 9.1-9.2

Autori: Neves, Aitana; Dolanski-Aghamanoukjan, Lorenz; Maier, Wolfgang; Pergl, Robert; Akerström, Wolmar Nyberg; Hjerde, Erik; Cuesta, Isabel; Popleteeva, Marina; Oulas, Anastasia; Mohamed, Anliat; Tonazzolli, Arianna; Pilvar, Diana; Calhoun, Erin; Åberg, Espen; Erard, Frédéric; Rasche, Helena; Messak, Imane; van Helden, Jacques; Lara, Maria; Rahman, Nadim; Karathanasis, Nestoras; Willassen, Nils-Pede
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8116380

ELIXIR-CONVERGE D8.5 Data access points and tools

Autori: Cochrane, Guy; Cummins, Carla; Rahman, Nadim; Ventouratou, Marianna
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.5938357

ELIXIR-CONVERGE D8.3 Raw sequence data processing workflow in operation

Autori: Cochrane, Guy; Rahman, Nadim; Sokolov, Alexey
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5140396

ELIXIR-CONVERGE D6.4 Project Handbook Final version and lessons learnt

Autori: Arenas Marquez, Juan; Coutts, Nikki; Hurst, Hannah
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8183281

ELIXIR-CONVERGE D7.4 Report on operational processes across the federated EGA network and data transfer with the European COVID-19 platform

Autori: Hornos Vidal, Albert; Portell Silva, Laura; Capella-Gutierrez, Salvador; Freeberg, Mallory; Curwin, Amy; Rambla, Jordi
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7274356

Progress on Data Stewardship Wizard during BioHackathon Europe 2020

Autori: Marek Suchánek, Rob Hooft, and Konogan Bourhy
Pubblicato in: BioHackrXiv Preprints, 2020
Editore: BioHackrXiv - Centre for Open Science
DOI: 10.37044/osf.io/9mnkb

Measuring outcomes and impact from the BioHackathon Europe

Autori: Leyla Jael Castro, Corinne Martin, Georgi Lazarov, Dana Cernoskova, Terue Takatsuki, Jennifer Harrow, Dietrich Rebholz-Schuhmann
Pubblicato in: BioHackrXiv Preprints, 2021
Editore: BioHackrXiv - Centre for Open Science
DOI: 10.37044/osf.io/3dxhg

ELIXIR-CONVERGE D3.4 Dissemination of the toolkit across the ERA

Autori: Alper, Pinar; Popleteeva, Marina; Martin, Corinne; Droesbeke, Bert; Cook, Martin; Westwick, Elaine; Goble, Carole; Coppens, Frederik; van Gelder, Celia; Balsyte, Erika; Tseng, Zippy
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7858238

ELIXIR-CONVERGE - D1.4 ELIXIR Best Practices recommendations

Autori: Berka, Karel; Waheed, Zahra; Mičetić, Ivan; Bösl, Korbinian; D'Anna, Flora; Kallberg, Yvonne; Lieby, Paulette; Buono, Rafael Andrade; Fatima, Nazeefa; Carraro, Marco; Tosatto, Silvio; Persson, Bengt; Vondrášek, Jirí; Jareborg, Niclas
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7503650

Research Data Management Toolkit (RDMkit): guidelines for plant phenotyping data management and sharing

Autori: Erwan Le Floch; Anne-Françoise Adam-Blondon; Isabelle Alic; Bert Droesbeke; Stijn Dhondt; Daniel Faria; Sebastian Beier; Pascal Neveu; Nicolas Francillonne; Célia Michotey; Cyril Pommier
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7148792

ELIXIR-CONVERGE D8.4 Phylogenetic tools and enhanced results visualisation

Autori: O'Cathail, Colman; Sokolov, Alexey; Rahman, Nadim; Cochrane, Guy; Ventouratou, Marianna
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5140285

ELIXIR-CONVERGE D2.2 Report on the ready-to-use training materials for usage and rolling-out in Task 2.3

Autori: van Gelder, Celia; Leskošek, Brane; Cardona, Alexia; Palagi, Patricia
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8168922

ELIXIR-CONVERGE D9.1 Report on mobilised sequence and variation data - relates to tasks 9.1-9.2

Autori: Cochrane, Guy; Waheed, Zahra; Rahman, Nadim; Ventouratou, Marianna; ELIXIR-CONVERGE
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8116157

Demonstrating public value to funders and other stakeholders—the journey of ELIXIR, a virtual and distributed research infrastructure for life science data

Autori: Corinne S. Martin,Susanna Repo,Juan Arenas Márquez,Niklas Blomberg,Katharina B. Lauer,Xènia Pérez Sitjà,Premysl Velek,Ana M. P. Melo,Christine Stansberg,Francesca De Leo,Elina Griniece,Hannes Rothe,Robert Petryszak,Andrew Smith
Pubblicato in: Wiley Online Library, Numero Volume 92, Numero 3, 2021
Editore: Wiley
DOI: 10.1111/apce.12328

ELIXIR-CONVERGE D1.1 Best Practices 1v0

Autori: Jareborg, Niclas; D'Anna, Flora; Hooft, Rob; B��sl, Korbinian; Kallberg, Yvonne; Faria, Daniel; Dominguez Del Angel, Victoria; Bianchini, Federico; Kronander, Elin; Englund, Marcus; Promponas, Vasilis; Vergoulis, Thanasis; Rossier, Gr��goire; Leiby, Paulette; Adler, Priit; Fuchs, Siiri; Ahokas, Minna; Persson, Bengt; ELIXIR Data Management Network
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4501946

De groeiende rol van digitale gegevens in het onderzoek

Autori: Hooft, Rob W.W.
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6358975

ELIXIR-CONVERGE D5.3 Report on the dedicated training and capacity building activities

Autori: Leskošek, Brane; Haurheeram, Vanita; Bianchini, Federico; Alper, Pinar; Portell-Silva, Laura; Åberg, Espen; Hospital, Adam; Popleteeva, Marina; Willassen, Nils P; Vidak, Marko; Adam-Blondon, Anne-Françoise; Collin, Olivier; Curwin, Amy; Freeberg, Mallory; Le Floch, Erwan; Lieby, Paulette; Picardi, Ernesto; Capella-Gutierrez, Salvador
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7858327

ELIXIR-CONVERGE D5.1 Categorisation of the pilot projects

Autori: Adam-Blondon, Anne-Françoise; Alper, Pinar; Capella-Gutierrez, Salvador; Faria, Daniel; Portell Silva, Laura; Hospital, Adam; Willassen, Nils-Peder
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4674491

Unsupervised classification of SARS-CoV-2 genomic sequences uncovers hidden genetic diversity and suggests an efficient strategy for genomic surveillance

Autori: Matteo Chiara, David S. Horner, Erika Ferrandi, Carmela Gissi, Graziano Pesole
Pubblicato in: bioRXiv Preprints, 2021
Editore: bioRXiv - Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.23.449558

ELIXIR-CONVERGE D2.5 Report on the outreach activities and training activities produced

Autori: Palagi, Patricia; Cardona, Alexia; Celia van Gelder; Leskošek, Brane
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8168646

ELIXIR-CONVERGE D5.4 Report on KPI

Autori: Adam-Blondon, Anne-Françoise; Portell-Silva, Laura; Capella-Gutierrez, Salvador; Popleteeva, Marina; Jonassen, Inge; Bianchini, Federico; Åberg, Espen; Hospital, Adam; Willassen, Nils-Peder; Sanz, Ferran; Picardi, Ernesto; Alper, Pinar; Ded, Vilém; Djenaba Barry, Nene; d'Altri, Teresa; Vidak, Marco; Martin, Corinne
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8116507

Making Canonical Workflow Building Blocks interoperable across workflow languages

Autori: Soiland-Reyes, Stian; Genís Bayarri; Andrio, Pau; Long, Robin; Lowe, Douglas; Niewielska, Ania; Hospital, Adam; Groth, Paul
Pubblicato in: Data Intelligence, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4602854

ELIXIR-CONVERGE D3.1 Assembled starter toolkit

Autori: Goble, Carole; Alper, Pinar; Droesbeke, Bert; D'Anna, Flora; Andrabi, Munazah; Jetten, Mijke; Coppens, Frederik; Hooft, Rob; Cook, Martin; van Gelder, Celia; Faria, Daniel; Jareborg, Niclas; Englund, Marcus; Kallberg, Yvonne; Wittig, Ulrike; B��sl, Korbinian; Jonassen, Inge; Child, Chris; Collin, Olivier; Bianchini, Federico; Berka, Karel; Perez Sitja, X��nia; Rossier, Gr��goire; Ben-A
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4501634

ELIXIR-CONVERGE D3.3 Single entry-point portal for the toolkit for all stakeholders

Autori: Hooft, Rob; D'Anna, Flora; Coppens, Frederik; Droesbeke, Bert
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7707623

ELIXIR-CONVERGE D5.5 Report on the remaining four DMP processes

Autori: Portell-Silva, Laura; Haurheeram, Vanita; Adam-Blondon, Anne-Françoise; Capella-Gutierrez, Salvador; Popleteeva, Marina; Bianchini, Federico; Åberg, Espen; Hooft, Rob; Schuánek, Marek; Slifka, Jan; Hospital, Adam; Willassen, Nils-Peder; Piñero, Janet; Sanz, Ferran; Ramirez-Anguita, Juan Manuel; Pastor, Manuel; Angel Mayer, Miguel; Picardi, Ernesto; Alper, Pinar; Ded, Vilém; Djenaba Barry, Nen
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8142800

Ready for BioData Management?

Autori: Ventura-Costa, Carolina; Oliveira, Jorge S.; Paixão, Tiago; Leite, Ricardo; Faria, Daniel; Melo, Ana M. P.
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7186474

ELIXIR-CONVERGE D5.2 Report on the first two DMP processes

Autori: Portell, Laura; Capella-Gutierrez, Salvador; Alper, Pinar; d'Altri, Teresa; Hospital, Adam; Åberg, Espen; Faria, Daniel; Adam-Blondon, Anne-Françoise; Collin, Olivier; Willassen, Nils-Peder; Lieby, Paulette; Oulas, Anastasis; Pafilis, Evangelos; Jareborg, Niclas; Fatima, Nazeefa; Åkerström, Wolmar Nyberg; Picardi, Ernesto
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5139903

ELIXIR-CONVERGE - D1.3 A pan-European model for data management in life sciences

Autori: Vondrášek, Jirí; Berka, Karel; Pižemová, Natália; Jareborg, Niclas; Carraro, Marco; Waheed, Zahra; Mičetić, Ivan; Jetten, Mijke
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7503690

ELIXIR-CONVERGE D7.5 Retrospective assessment of national use-cases, identification of gaps, and recommendations for future Federated EGA roadmap

Autori: Keane, Thomas; Freeberg, Mallory; D'Altri, Teresa; Curwin, Amy
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8116078

ELIXIR-CONVERGE D3.2 Toolkit extension based on first wave demonstrators

Autori: Jonassen, Inge; Bösl, Korbinian; Goble, Carole; Alper, Pinar; Droesbeke, Bert; D'Anna, Flora; Faria, Daniel; Andrabi, Munazah; Coppens, Frederik; Cook, Martin; Jareborg, Niclas; Wittig, Ulrike; Portell Silva, Laura; Jetten, Mijke; Hooft, Rob; Bianchini, Federico; van Gelder, Celia; Fuchs, Siiri; Ahokas, Minna; Kallberg, Yvonne; Collin, Olivier; Berka, Karel; Williams, Alan R; Englund, Markus; Car
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5139897

ELIXIR-CONVERGE D2.1 Report on the identified training needs and a timeline for training courses

Autori: Cardona, Alexia; van Gelder, Celia; Palagi, Patrícia; Leskošek, Brane
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4892862

FAIR+E Pathogen data for surveillance and research: lessons from COVID-19

Autori: Neves, Aitana; Cuesta, Isabel; Hjerde, Erik; Salgado, David; van Helden, Jacques; Rahman, Nadim; Fatima, Nazeefa; Karathanasis, Nestoras; Zmora, Pawel; Nyberg Åkerström, Wolmar; Nagaraja Grellscheid, Sushma; Waheed, Zahra; Blomberg, Niklas; ELIXIR CONVERGE WP9 community
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8138316

ELIXIR-CONVERGE D9.3 Best practices documents on data standards - relates to task 9.3

Autori: Monzón Fernández, Sara; Nyberg Åkerström, Wolmar; Lara, María; Cuesta de la Plaza, Isabel; Neves, Aitana; Mohamed, Anliat; Salgado, David; Pilvar, Diana; Inno, Heleri; Messak, Imane; van Helden, Jacques; Willassen, Nils-Peder; Denecker, Thomas; Pergl, Robert; Suchánek, Marek
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8177166

ELIXIR-CONVERGE D7.1 Report of use-cases and architecture for the EGA federation

Autori: Keane, Thomas; Freeberg, Mallory; Kerry, Giselle; Rambla, Jordi; Morello, Francesca; Eufinger, Jan; Gu, Wei
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4893063

ELIXIR-CONVERGE D4.1 Industry engagement WIKI guide for ELIXIR Nodes

Autori: Sousoni, Despoina; Lauer, Katharina; Martin, Corinne; Haskell, Erin; Perez Sitja, Xènia; Westwick, Elaine; Tseng, Zippy; Cernoskova, Dana; Balzano, Melissa; Portugal Melo, Ana; de Leo, Francesca; de Ruyck, Kim; Maisinger, Klaus; Smith, Andrew
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6822169

ELIXIR-CONVERGE: D2.3 - 1st Report on delivered data management and stewardship courses

Autori: Leskošek, Brane; Cardona, Alexia; van Gelder, Celia; Palagi, Patricia; WP2 Members
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6642066

ELIXIR-CONVERGE D7.3 COVID-19 metadata mapping model across COVID-19 studies in federated EGA

Autori: Morello, Francesca; Lehväslaiho, Heikki; Lappalainen, Ilkka; Rambla, Jordi
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4893221

ELIXIR-CONVERGE: Annex 1 to Deliverable D5.1 - User Stories_v1

ELIXIR-CONVERGE D3.5 Extended toolkit

Autori: Coppens, Frederik; D'Anna, Flora; Droesbeke, Bert; Fatima, Nazeefa; Goble, Carole; Jareborg, Niclas; Hooft, Rob; Suchánek, Marek; Pergl, Robert
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8144240

ELIXIR-CONVERGE D6.3 Project Handbook 2v0

Autori: Arenas Marquez, Juan; Coutts, Nikki; Hurst, Hannah; Wingender, Joana
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5146094

ELIXIR-CONVERGE D4.2 Updated ELIXIR Long-term Sustainability Plan

Autori: Smith, Andrew; Martin, Corinne; Balsyte, Erika; Sousoni, Despoina
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8116122

ELIXIR-CONVERGE D6.1 Project Handbook 1v0

Autori: Hurst, Hannah; Arenas Marquez, Juan; Coutts, Nikki
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3855685

ELIXIR-CONVERGE D8.2 Workshop to explore and plan the inclusion of tools and data from projects that have diverted towards COVID-19 research

Autori: Rinck, Gabriele; Cochrane, Guy; Ventouratou, Marianna
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4722885

ELIXIR-CONVERGE D2.4 2nd Report on delivered data management and stewardship courses

Autori: Leskošek, Brane; Cardona, Alexia; van Gelder, Celia; Palagi, Patricia
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8186990

Workshop on data management and data deposition for biological images

Autori: Tatiana Woller; Alexander Botzki; Sebastian Munck
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7193957

Data Stewardship Wizard: Selecting suitable FAIR practices early in a project.

Autori: Hooft, Rob
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7502201

ELIXIR-CONVERGE - PILOT USE OF THE ELIXIR PROJECT MONITORING TOOL BY ELIXIR-PORTUGAL

Autori: Santos, Rafael; Melo, Ana Portugal; Arenas Marquez, Juan; Hurst, Hannah; Coutts, Nikki
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4522175

The Portuguese experience in enabling interoperability frameworks for scientific data

Autori: Melo, Ana M. P.
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4916620

Data Stewardship Wizard: philosophy and Implementation

Autori: Rob W.W. Hooft
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6010328

Metabolomics and Integrative Omics: from data production to analysis

Autori: Leonardo Tenori; Lars Ove Dragsted; Stefania Savoi; Igor Fochi; Pietro Franceschi; Duccio Cavalieri; Christoph Steinbeck; Veronica Ghini; Danilo Porro; Anna Maria Timperio; Bruno Fosso; Fabrizio Mastrorocco; Daniela Gaglio; Giuseppina Fanelli; Sergio Giannattasio; Clara Musicco
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6522068

Flanders Bio Imaging – towards efficient centralized research data management and analysis of bioimaging data

Autori: Munck, Sebastian; Christopher Cawthorne; Tatiana Woller; Benjamin Pavie; Alexander Botzki; Frank Vernaillen; Raf De Coster; Paul Borgermans; Ingrid Barcena Roig; Mariana Montes
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7990100

The landscape of FAIR and Open Science in Portugal and Beyond

Autori: Eloy Rodrigues
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6560879

Fellowship of the Data — RDM Trainer Network Meeting 2023: Presentations

Autori: Wilbrandt, Jeanne; Biernacka, Katarzyna; Lübke, Nils-Christian; Schnitzer, Helena; Wibberg, Daniel; Frisch, Katrin
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8117453

Research Data Management in Life Sciences: Preserve, publish and share your data

Autori: Botzki, Alexander
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4322967

The Portuguese Local European Genome-Phenome Archive (EGA)

Autori: Jorge S. Oliveira; Fernando Mira da Silva; José Luís Oliveira; Mário Silva; Ana M. P. Melo
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7186541

Building Research Data Management (RDM) expertise and training resources in ELIXIR Nodes

Autori: Celia W.G. van Gelder; Patricia Palagi; Alexia Cardona; Brane Leskošek
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8348286

First steps on a FAIR Journey

Autori: Hooft, Rob W.W.
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5679792

First Steps in making your data FAIR

Autori: Hooft, Rob
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5769649

Testing the Application of ELIXIR Plant Standards in the Industry

Autori: Melo, Ana M. P.; Faria, Daniel
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4916544

Research Data Management in Life Sciences: Re-using existing data

Autori: Botzki, Alexander
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4322980

Involvement of the Catecholamine Pathway in Glioblastoma Development

Autori: Zoltán Kraboth; Bela Kajtár; Bence Gálik; Attila Gyenesei; Attila Miseta; Bernadette Kalman
Pubblicato in: Cells, Numero 2021 Mar; 10(3): 549., 2021, ISSN 2073-4409
Editore: Europe PMC
DOI: 10.3390/cells10030549

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing

Autori: Peter W Harrison, Rodrigo Lopez, Nadim Rahman, Stefan Gutnick Allen, Raheela Aslam, Nicola Buso, Carla Cummins, Yasmin Fathy, Eloy Felix, Mihai Glont, Suran Jayathilaka, Sandeep Kadam, Manish Kumar, Katharina B Lauer, Geetika Malhotra, Abayomi Mosaku, Ossama Edbali, Young Mi Park, Andrew Parton, Matt Pearce, Jose Francisco Estrada Pena, Joseph Rossetto, Craig Russell, Sandeep Selvakumar, Xènia P
Pubblicato in: Nucleic Acids Research, Numero Volume 49, Numero W1, 2021, Pagina/e 619-623, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab417

CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

Autori: Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David S Horner, Graziano Pesole
Pubblicato in: Bioinformatics, Numero Volume 36, Numero 22-23, 2020, Pagina/e 5522-5523, ISSN 1460-2059
Editore: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1047

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis

Autori: Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen McDonagh, Paul Flicek, Johanna McEntyre, Ewan Birney, Rolf Apweiler
Pubblicato in: Nucleic Acids Research, Numero Volume 49, Numero D1, 2021, Pagina/e 29-37, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1077

Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities

Autori: Matteo Chiara, Anna Maria D’Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David S Horner, Graziano Pesole
Pubblicato in: Briefings in Bioinformatics, Numero Volume 22, Numero 2, 2021, Pagina/e 616-630, ISSN 1477-4054
Editore: Oxford University Press
DOI: 10.1093/bib/bbaa297

The European Nucleotide Archive in 2020.

Autori: Peter W. Harrison; Alisha Ahamed; Raheela Aslam; Blaise T. F. Alako; Josephine Burgin; Nicola Buso; Mélanie Courtot; Jun Fan; Dipayan Gupta; Muhammad Haseeb; Sam Holt; Talal Ibrahim; Eugene Ivanov; Suran Jayathilaka; Vishnukumar Balavenkataraman Kadhirvelu; Manish Kumar; Rodrigo Lopez; Simon Kay; Rasko Leinonen; Xin Liu; Colman O’Cathail; Amir Pakseresht; Youngmi Park; Stephane Pesant; Nadim Ra
Pubblicato in: Nucleic Acids Research, Numero 21, 2021, Pagina/e D82-D85, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1028

Assessing the Impact of SARS-CoV-2 Lineages and Mutations on Patient Survival

Autori: Loucera, Carlos; Perez-Florido, Javier; Casimiro-Soriguer, Carlos S; Ortuño, Francisco M; Carmona, Rosario; Bostelmann, Gerrit; Martínez-González, L Javier; Muñoyerro-Muñiz, Dolores; Villegas, Román; Rodriguez-Baño, Jesus; Romero-Gomez, Manuel; Lorusso, Nicola; Garcia-León, Javier; Navarro-Marí, Jose M; Camacho-Martinez, Pedro; Merino-Diaz, Laura; Salazar, Adolfo de; Viñuela, Laura; The
Pubblicato in: Viruses; Volume 14; Numero 9; Pages: 1893, Numero 1, 2022, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14091893

Comparative Genomics Reveals Early Emergence and Biased Spatiotemporal Distribution of SARS-CoV-2

Autori: Matteo Chiara, David S Horner, Carmela Gissi, Graziano Pesole
Pubblicato in: Molecular Biology and Evolution, Numero Volume 38, Numero 6, 2021, Pagina/e 2547-2565, ISSN 1537-1719
Editore: Oxford University Press
DOI: 10.1093/molbev/msab049

Connecting data, tools and people across Europe: ELIXIR’s response to the COVID-19 pandemic

Autori: Niklas Blomberg; Katharina B. Lauer
Pubblicato in: European Journal of Human Genetics, Numero 28, 2021, Pagina/e 718-723, ISSN 1476-5438
Editore: Springer Nature
DOI: 10.1038/s41431-020-0637-5

REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments

Autori: Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignanò, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi
Pubblicato in: Nucleic Acids Research, Numero Volume 49, Numero D1, 2021, Pagina/e 1012-1019, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa916

The road to success: drawing parallels between 'road' and 'research data' infrastructures to foster understanding between service providers, funders and policymakers

Autori: Corinne Martin; Rob Hooft
Pubblicato in: F1000Research, Numero 1, 2023, ISSN 2046-1402
Editore: F1000 Research Ltd.
DOI: 10.12688/f1000research.128167.2

DNA CpG methylation in sequential glioblastoma specimens

Autori: Zoltan Kraboth; Bence Galik; Marton Tompa; Bela Kajtar; Peter Urban; Attila Gyenesei; Attila Miseta; Bernadette Kalman
Pubblicato in: Journal of Cancer Research and Clinical Oncology, 2020, ISSN 1432-1335
Editore: Springer
DOI: 10.1007/s00432-020-03349-w

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