Project Deliverables & Publications

The following scientific publications are at least partially funded via EOSC-Life, Grant Agreement No. 824087:

•  The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform.

Bray, S.A., Lucas, X., Kumar, A. et al. J Cheminform 12, 40 (2020), https://doi.org/10.1186/s13321-020-00442-7.
The ChemicalToolbox is used within EOSC-Life’s Demonstrator 1 (Galaxy team).

• Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling / GigaScience 8/12, https://doi.org/10.1093/gigascience/giz143

• Measuring local-directional resolution and local anisotropy in cryo-EM maps

Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano Nature Communications 11/1, https://doi.org/10.1038/s41467-019-13742-w

• Experiment design driven FAIRification of omics data matrices, an exemplar

Philippe Rocca-Serra, Susanna-Assunta Sansone Scientific Data 6/1, https://doi.org/10.1038/s41597-019-0286-0

• Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity

Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff Frontiers in Immunology 10, 10.3389/fimmu.2019.03091

• FAIR Computational Workflows

Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober Data Intelligence 2/1-2 Yes 10.1162/dint_a_00033

• Evaluating FAIR maturity through a scalable, automated, community-governed framework

Mark D. Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto, Dominique Batista, Peter McQuilton, Tobias Kuhn, Philippe Rocca-Serra, Mercѐ Crosas, Erik Schultes Scientific Data 6/1 10.1038/s41597-019-0184-5

• FAIRness Literacy: The Achilles’ Heel of Applying FAIR Principles

Romain David, Laurence Mabile, Alison Specht, Sarah Stryeck, Mogens Thomsen, Mohamed Yahia, Clement Jonquet, Laurent Dollé, Daniel Jacob, Daniele Bailo, Elena Bravo, Sophie Gachet, Hannah Gunderman, Jean-Eudes Hollebecq, Vassilios Ioannidis, Yvan Le Bras, Emilie Lerigoleur, Anne Cambon-Thomsen Data Science Journal 19 DOI: 10.5334/dsj-2020-032

• Exploration of databases and methods supporting drug repurposing: a comprehensive survey

Ziaurrehman Tanoli, Umair Seemab, Andreas Scherer, Krister Wennerberg, Jing Tang, Markus Vähä-Koskela, Briefings in Bioinformatics, bbaa003, DOI: 10.1093/bib/bbaa003

• FlexAlign: An Accurate and Fast Algorithm for Movie Alignment in Cryo-Electron Microscopy

Střelák, David; Filipovič, Jiří; Jiménez-Moreno, Amaya; Carazo, Jose M.; Sánchez Sorzano, Carlos Ó. 2020, Electronics 9, no. 6: 1040.  DOI: 10.3390/electronics9061040

• Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures

Roberto Melero; Carlos Oscar S. Sorzano; Brent Foster; José-Luis Vilas; Marta Martínez; Roberto Marabini; Erney Ramírez-Aportela; Ruben Sanchez-Garcia; David Herreros; Laura del Caño; Patricia Losana; Yunior C. Fonseca-Reyna; Pablo Conesa; Daniel Wrapp; Pablo Chacon; Jason S. McLellan; Hemant D. Tagare; Jose-Maria Carazo, IUCrJ, DOI: 10.1101/2020.07.08.191072

• 39 Hints to Facilitate the Use of Semantics for Data on Agriculture and Nutrition

Caracciolo, C., Aubin, S., Jonquet, C., Amdouni, E., David, R., Garcia, L., Whitehead, B., Roussey, C., Stellato, A. and Villa, F.  Data Science Journal, 2020, 19(1), p.47. DOI: 10.5334/dsj-2020-047

• Making experimental data tables in the life sciences more FAIR: a pragmatic approach

Daniel Jacob, Romain David, Sophie Aubin, Yves Gibon. GigaScience, Volume 9, Issue 12, December 2020, giaa144, 10.1093/gigascience/giaa144

• A Marine Biodiversity Observation Network for Genetic Monitoring of Hard-Bottom Communities (ARMS-MBON)

Obst Matthias, Exter Katrina, Allcock A. Louise, Arvanitidis Christos, Axberg Alizz, Bustamante Maria, Cancio Ibon, et al. Frontiers in Marine Science, Frontiers Media, 2020, 7, 10.3389/fmars.2020.572680

• Towards FAIRification of experimental data tables in life sciences: a pragmatic approach

Bernillon, Stéphane; Cabasson, Cecile; CASSAN, Cédric; Da Costa, Grégory; Deborde, Catherine; Flandin, Amélie; Fouillen, Laetitia; Gibon, Yves; Jacob, Daniel; Moing, Annick; Mongrand, Sebastien; Pedrot, Eric; Petriacq, Pierre; Prigent, Sylvain; Renouf, Elodie; Richard, Tristan; Rolin, Dominique; Rouger, Caroline; Valls, Josep; Van Delft, Pierre https://hal.inrae.fr/hal-02570809 10.15454/1.5572412770331912E12

• Non-repudiable provenance for clinical decision support systems

Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa http://arxiv.org/abs/2006.11233

• Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial

Bray, Simon A.; Senapathi, Tharindu; Barnett, Christopher B.; Grüning, Björn A. BioRxiv 10.1101/2020.05.08.084780

• FSC-Q: A CryoEM map-to-atomic model quality validation based on the local Fourier Shell Correlation

Ramirez-Aportela, Erney; Maluenda, David; Fonseca, Yunior C.; Conesa, Pablo; Marabini, Roberto; Heymann, J. Bernard; Carazo, Jose Maria; Sorzano, Carlos Oscar S. BioRxiv 10.1101/2020.05.12.069831

• The WorkflowHub – a registry for workflows. The Bioschemas workflow profile

Carole Goble 10.5281/zenodo.4012124

• ECRIN Clinical Research Metadata Schema Version 4.0 (September 2020) Appendices

Canham, Steve 10.5281/zenodo.4028900

• Packaging workflows with RO-Crate

Stian Soiland-Reyes; Ignacio Eguinoa 10.5281/zenodo.4011999

• Multitarget Virtual Screening for Drug Repurposing in COVID19

Sorzano, Carlos Oscar; Crisman, Enrique; Carazo, Jose Maria; Leon, Rafael 10.26434/chemrxiv.12652997.v2

EOSC-Life encompasses 34 deliverables, all but 1 of which are public. Deliverables will be uploaded here as soon as published:

• Deliverable D5.1 – Access and User Management System for Life Science – The Blueprint (Sep 2019)
• Deliverable D9.1 — Final report of analysis of the training needs of different EOSC-Life users (Feb 2020)
• Deliverable D6.1 – FAIR Requirements Document  (March 2020)
• Deliverable D4.2 — Report on requirements for regulatory compliance of sensitive health data and biological and medical research data (May 2020)
• Deliverable D1.1 — EOSC Cloud feasibility assessment for Demonstrators (Aug 2020)
• Deliverable D7.1 — Initial EOSC-LS Cloud Observatory Report (Aug 2020)
• Deliverable D12.1 (Confidential) (Aug 2020)
• Deliverable D2.1 — Cloud implementation of exemplary workflows (Aug 2020)
• Deliverable D11.1 — Data Management Plan (Aug 2020)
• Deliverable D3.1 — Publication of generic guidelines for the organization of topic-specific Open Calls (Sep 2020)
• Deliverable D14.1 — Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures (Oct 2020)
• Deliverable D9.2 — Review of EOSC-Life training activities, their impact and potential adaptations (Feb 2021)
• Deliverable D10.1 — Strategic Marketing and Stakeholder Mapping Report (Feb 2021)
• Deliverable D4.3 — Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples (March 2021)

Newsletter 1 – 14 Nov 2020

Newsletter 2 – 10 Feb 2020

Newsletter 3 . AGM – 27 Feb 2020

Newsletter 4 – 27 April 2020

Newsletter 5- 29 June 2020

Newsflash – 2nd Training Open Call – 10 Sept 2020

Newsflash – Digital Life Sciences Open Call – 15 Sept 2020

Newsletter 6 – 22 Oct 2020

Newsletter 7 – 16 Dec 2020

Newsletter 8 – 11 Feb 2021

Subscribe to our newsletter

• Provenance Week 2020 Poster: ISO 23494: Biotechnology – Provenance Information Model for Biological Specimen and Data

Wittner, Rudolf; Holub, Petr; Geiger, Jörg; Müller, Heimo; Goble, Carole; Soiland-Reyes, Stian; Fairweather, Elliot; Pirredu, Luca; Frexia, Francesca; Mascia, Cecilia; Zanetti, Gianluigi; Nakae, Hiroki; Strambio, Caterina; Moore, Josh; Grunwald, David; Swedlow, Jason 4th Provenance Week 2020 10.5281/zenodo.3901011

EOSC-Life version here.

• Issues and obstacles to the sharing of sensitive data in Europe, who are the stakeholders and what are their responsibilities?

David, Romain, Richard, Audrey, Stepanyann, Diana, Versteeg, Krista, Mineau-Cesari, Jonathan, Mistou, Michel-Yves, … Raoul, Hervé. (2020). Issues and obstacles to the sharing of sensitive data in Europe, who are the stakeholders and what are their responsibilities ? (Version 1.0). Presented at the CODATA and GO FAIR International FAIR Convergence Symposium (FAIR Convergence Symposium), France, 10.5281/zenodo.4293611

Presented at:

• RDA’s 16th Plenary – remotely, “Knowledge Ecology”, (RDA P16), Costa Rica, 09 – 12 November 2020 (Session Poster)
• CODATA and GO FAIR International FAIR Convergence Symposium (FAIR Convergence Symposium), France, 27 November – 4 December 2020 (Session Poster, Poster 63)

• The main European initiatives for sharing data and other research results in support of the scientific community. ELIXIR (Covid-19 data portal), OpenAIRE, RDA. Second edition

Allegra Via. Presentation given during the second edition of the webinar “Covid-19 e condivisione dei dati: perché in Italia si fa troppo poco?” belonging to the event series “Open Science e Covid-19. Collaborare per contrastare la pandemia”, on November 16th, 2020.

• Enabling & stimulating submission to the COVID data portal & re-use of the data

Frederik Coppens. Presentation on the status and progress in Belgium at the monthly meeting on the COVID-19 Data Portal organised by EMBL-EBI and the European Commission. This represents the status in November 2020, focussing on the development of tools to submit data to ENA. A command-line application was developed which was made available in Galaxy. Additionally containers have been generated to easily run the application locally.

• How in silico methods and data reuse can help reduce the number of animal experiments

Maddalena Fratelli. Presentation at the conference  “Towards replacement of animals for scientific purposes” ,  2-3 February 2021. Talking about machine learning to develop models of drug sensitivity prediction, (Q)SAR models of toxicity prediction and the role of data re-use in enhancing external validity of the studies.

 

Through its cluster projects, ESCAPE, ENVRI-FAIR, SSHOC, PaNOSC and EOSC-Life, the European Strategy Forum on Research Infrastructures (ESFRI) steers the integration and consolidation of thematic e-infrastructure platforms in preparation for connecting them to EOSC. The need to leverage domain expertise and better drive the innovation which research communities require can be found in these position papers reflecting current views and expectations about EOSC and the contributions of ESFRI to the European data infrastructure. An executive summary and overview table provide insights into the views of some of the most important research infrastructures in Europe on the future EOSC.

You can read the collection of the five position papers on Zenodo at this link: https://zenodo.org/record/3675081

The European Open Science Cloud (EOSC) will “enable a trusted, virtual, federated environment in Europe to store, share and reuse digital outputs from research (including publications, data, metadata and software) across borders and scientific disciplines”1. Today, at the end of 2020, many building blocks are in place and on-going EOSC projects endeavour to enrich the EOSC ecosystem. To ensure strong engagement by research communities, we believe that this is the time to re-orient the EOSC activities towards higher relevance for these communities.

The Science Clusters ENVRI-FAIR , EOSC-LIFE , ESCAPE , PaNOSC , SSHOC bring together 72 world-class research infrastructures from the ESFRI roadmap and beyond to work on FAIR data management and connecting their user communities to the EOSC. The European e-infrastructures EGI , EUDAT , GÉANT , and OpenAIRE provide inclusive services across Europe and beyond to the benefit of science.

Link to article