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

Deliverables

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

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

Phylogenetic tools and enhanced results visualisation

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

Report on the first two DMP process

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

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

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 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

Project Handbook 2v0

Update of the Project Handbook including update on the KPIs

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

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

Searching for OpenAIRE data...

Publications

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

Author(s): Rambla, Jordi; D'Altri, Teresa; Haziza, Frédéric
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4893190

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

Author(s): Cochrane, Guy; Rahman, Nadim; Sokolov, Alexey
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5140396

Progress on Data Stewardship Wizard during BioHackathon Europe 2020

Author(s): Marek Suchánek, Rob Hooft, and Konogan Bourhy
Published in: BioHackrXiv Preprints, 2020
Publisher: BioHackrXiv - Centre for Open Science
DOI: 10.37044/osf.io/9mnkb

Measuring outcomes and impact from the BioHackathon Europe

Author(s): Leyla Jael Castro, Corinne Martin, Georgi Lazarov, Dana Cernoskova, Terue Takatsuki, Jennifer Harrow, Dietrich Rebholz-Schuhmann
Published in: BioHackrXiv Preprints, 2021
Publisher: BioHackrXiv - Centre for Open Science
DOI: 10.37044/osf.io/3dxhg

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

Author(s): O'Cathail, Colman; Sokolov, Alexey; Rahman, Nadim; Cochrane, Guy; Ventouratou, Marianna
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5140285

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

Author(s): 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
Published in: Wiley Online Library, Volume 92, Issue 3, 2021
Publisher: Wiley
DOI: 10.1111/apce.12328

ELIXIR-CONVERGE D1.1 Best Practices 1v0

Author(s): 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
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4501946

ELIXIR-CONVERGE D5.1 Categorisation of the pilot projects

Author(s): Adam-Blondon, Anne-Françoise; Alper, Pinar; Capella-Gutierrez, Salvador; Faria, Daniel; Portell Silva, Laura; Hospital, Adam; Willassen, Nils-Peder
Published in: 2021
Publisher: 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

Author(s): Matteo Chiara, David S. Horner, Erika Ferrandi, Carmela Gissi, Graziano Pesole
Published in: bioRXiv Preprints, 2021
Publisher: bioRXiv - Cold Spring Harbor Laboratory
DOI: 10.1101/2021.06.23.449558

Making Canonical Workflow Building Blocks interoperable across workflow languages

Author(s): Soiland-Reyes, Stian; Genís Bayarri; Andrio, Pau; Long, Robin; Lowe, Douglas; Niewielska, Ania; Hospital, Adam; Groth, Paul
Published in: Data Intelligence, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4602854

ELIXIR-CONVERGE D3.1 Assembled starter toolkit

Author(s): 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
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4501634

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

Author(s): 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
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5139903

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

Author(s): Cardona, Alexia; van Gelder, Celia; Palagi, Patrícia; Leskošek, Brane
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4892862

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

Author(s): Keane, Thomas; Freeberg, Mallory; Kerry, Giselle; Rambla, Jordi; Morello, Francesca; Eufinger, Jan; Gu, Wei
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4893063

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

Author(s): Morello, Francesca; Lehväslaiho, Heikki; Lappalainen, Ilkka; Rambla, Jordi
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4893221

ELIXIR-CONVERGE D6.3 Project Handbook 2v0

Author(s): Arenas Marquez, Juan; Coutts, Nikki; Hurst, Hannah; Wingender, Joana
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5146094

ELIXIR-CONVERGE D6.1 Project Handbook 1v0

Author(s): Hurst, Hannah; Arenas Marquez, Juan; Coutts, Nikki
Published in: 2020
Publisher: 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

Author(s): Rinck, Gabriele; Cochrane, Guy; Ventouratou, Marianna
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4722885

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

Author(s): Santos, Rafael; Melo, Ana Portugal; Arenas Marquez, Juan; Hurst, Hannah; Coutts, Nikki
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4522175

The Portuguese experience in enabling interoperability frameworks for scientific data

Author(s): Melo, Ana M. P.
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4916620

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

Author(s): Botzki, Alexander
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4322967

First steps on a FAIR Journey

Author(s): Hooft, Rob W.W.
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5679792

First Steps in making your data FAIR

Author(s): Hooft, Rob
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5769649

Testing the Application of ELIXIR Plant Standards in the Industry

Author(s): Melo, Ana M. P.; Faria, Daniel
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4916544

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

Author(s): Botzki, Alexander
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4322980

Involvement of the Catecholamine Pathway in Glioblastoma Development

Author(s): Zoltán Kraboth; Bela Kajtár; Bence Gálik; Attila Gyenesei; Attila Miseta; Bernadette Kalman
Published in: Cells, 2021 Mar; 10(3): 549., 2021, ISSN 2073-4409
Publisher: 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

Author(s): 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
Published in: Nucleic Acids Research, 13624962, 2021, Page(s) 619-623, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab417

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

Author(s): Matteo Chiara, Federico Zambelli, Marco Antonio Tangaro, Pietro Mandreoli, David S Horner, Graziano Pesole
Published in: Bioinformatics, Volume 36, Issue 22-23, 2020, Page(s) 5522-5523, ISSN 1460-2059
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btaa1047

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

Author(s): Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen McDonagh, Paul Flicek, Johanna McEntyre, Ewan Birney, Rolf Apweiler
Published in: Nucleic Acids Research, Volume 49, Issue D1, 2021, Page(s) 29-37, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1077

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

Author(s): 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
Published in: Briefings in Bioinformatics, Volume 22, Issue 2, 2021, Page(s) 616-630, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa297

The European Nucleotide Archive in 2020.

Author(s): 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
Published in: Nucleic Acids Research, 21, 2021, Page(s) D82-D85, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa1028

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

Author(s): Matteo Chiara, David S Horner, Carmela Gissi, Graziano Pesole
Published in: Molecular Biology and Evolution, Volume 38, Issue 6, 2021, Page(s) 2547-2565, ISSN 1537-1719
Publisher: Oxford University Press
DOI: 10.1093/molbev/msab049

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

Author(s): Niklas Blomberg; Katharina B. Lauer
Published in: European Journal of Human Genetics, 28, 2021, Page(s) 718-723, ISSN 1476-5438
Publisher: Springer Nature
DOI: 10.1038/s41431-020-0637-5

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

Author(s): Luigi Mansi, Marco Antonio Tangaro, Claudio Lo Giudice, Tiziano Flati, Eli Kopel, Amos Avraham Schaffer, Tiziana Castrignanò, Giovanni Chillemi, Graziano Pesole, Ernesto Picardi
Published in: Nucleic Acids Research, Volume 49, Issue D1, 2021, Page(s) 1012-1019, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa916

DNA CpG methylation in sequential glioblastoma specimens

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