Providing an open collaborative space for digital biology in Europe

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

FAIRassist software
Cloud implementation of exemplary workflows selected by the RIs/communities

Cloud implementation of exemplary workflows selected by the RIs/communities including demonstrators

Implementation of a mechanism for publishing and sharing workflows across instances of the environment

Implementation of a comprehensive workflow registry solution for publishing and sharing workflows across instances of the Tools Collaboratory

A common environment that can run cross-RIs workflows

A common environment (Tools Collaboratory) that can run cross-RIs workflows following the hackathons/workshops/WP3 use cases

Report on reproducibility
Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples

Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data including imaging cohort integration and biosamples

Summary of EOSC-Life Main Achievements, Impacts, and Sustainability and Exploitation Plans

Summary of EOSCLife Main Achievements Impacts and Sustainability and Exploitation Plans

Access and User Management System for Life Science (LS AAI) - final implementation and usage report

Access and User Management System for Life Science LS AAI final implementation and usage report

Project plan for optional services and future cooperation with IDDO

Results of exploration for cooperation with IDDO regarding possible optional services including services for the conversion of datasets to a common standard CDISC as well as data integration supporting patientlevel metaanalyses

Access and User Management System for Life Science - the blueprint: 2nd update

Access and User Management System for Life Science the blueprint 2nd update of the initial document

Review of EOSC-Life training activities, their impact and potential adaptations

Review of EOSCLife training activities their impact and potential adaptations

Report on a methodology framework to assess reproducibility
Common Framework for Quality, Data and Service Management

Common Framework for Quality Data and Service Management

Report about use and user satisfaction of COVID-19 repository including a maintenance and sustainability plan

Report about use and user satisfaction of COVID19 repository including a maintenance and sustainability plan

EOSC FAIR services deployment for open call
Report on requirements for regulatory compliance of sensitive health data and biological and medical research data management
Report on data standards for observational and interventional studies, and on interoperability between healthcare and research data

Report on data standards for observational and interventional studies and on interoperability between healthcare and research data

Enhanced COVID-19 Portal and data mobilisation reporting

COVID19 Portal operating systematic data harvesting systems and tools to provide statistics from comprehensive EMBLEBI data resources and tracking of growing data sets offering tools and programmatic access having undergone User Experience testing

Requirements for hosting/distributing and access control for sensitive data

Requirements for hostingdistributing and access control for sensitive data

FAIR Requirements document

Requirements document available

Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures

Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures.

Review of effectiveness and impact of outreach and stakeholder engagement
EOSC Cloud feasibility assessment for demonstrators
Common provenance model for processing biological material, data generation and computational workflows

Common provenance model for processing biological material data generation and computational workflows

Final report on EOSC-Life training activities and their impact

Final report on EOSCLife training activities and their impact

Summary Report Stakeholder Forum Meetings
Report on identification and application of registries for FAIR data infrastructures
Access and User Management System for Life Science (LS AAI) – the blueprint
Data mobilisation summary

Summary of mobilised data to date highlighting data platforms formats levels of assembly and national contributions

Publication of generic guidelines for the organization of topic-specific Open Calls

Publication of generic guidelines for the organisation of topic-specific Open Calls

Access and User Management System for Life Science - the blueprint: 1st update

Access and User Management System for Life Science the blueprint 1st update of the initial document

Provenance proposed model

Provenance proposed model available

Access and User Management System for Life Science (LS AAI) - the implementation and usage report

Access and User Management System for Life Science LS AAI the implementation and usage report

Life Science in EOSC: Summary of EOSC-Life impact and key results

Life Science in EOSC Summary of EOSCLife impact and key results

Report about technical implementation and validation of the COVID-19 portal

Report about technical implementation and validation of the COVID19 portal

Initial EOSC-LS Cloud Observatory Report

The report will detail the support mechanisms available to the BMS RIs and how the allocated cloud resources have been used so far by the BMS RIs. It will analyse the activities to date and provide recommendations on how the service can be evolved during the rest of the project.

EOSC Sustainability best practice
Final EOSC-LS Cloud Observatory Report

The report will detail the support mechanisms available to the BMS RIs and how the allocated cloud resources have been used so far by the BMS RIs It will analyse the activities to date and provide recommendations on how the service can be evolved during the rest of the project

Report on the work of the Open Call Projects
Strategic Marketing and Stakeholder mapping report
Report on the work of the initial Demonstrators
EOSC repository deployment for project demonstrators
Final report of analysis of the training needs of different EOSC-Life users

Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes

FAIRsharing webpage

Launch of FAIRsharing webpage

EOSC-Life Data Management Plan

EOSC-Life Data Management Plan: WP11 will deliver a data management plan in collaboration with WP4 (ethics and legal) to provide further evidence of appropriate ethics committees and competent authorities. EOSC-life’s SEAB will consist of an ethics expert who will be consulted on this specific deliverable.

Publications

Removing Barriers to Reproducible Research in Archaeology

Author(s): Karoune, Emma; Plomp, Esther
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6618672

EOSC-Life Report on data standards for observational and interventional studies, and interoperability between healthcare and research data

Author(s): Canham, Steve; Ohmann, Christian; Boiten, Jan-Willem; Panagiotopoulou, Maria; Hughes, Nigel; David, Romain; Sanchez Pla, Alex; Maxwell, Lauren; Aerts, Jozef; Facile, Rhonda; Griffon, Nicolas; Saunders, Gary; van Bochove, Kees; Ewbank, Jonathan
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5810611

Introduction to Semantic Interoperability Challenges for RIs

Author(s): David, Romain; Madon, Bénédicte; Torralba, Antonio
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8059821

Non-repudiable provenance for clinical decision support systems

Author(s): Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Published in: 2021
Publisher: ArXiv
DOI: 10.48550/arxiv.2006.11233

EOSC-Life WP14: COVID-19 Repository Data Sharing Policy

Author(s): Ohmann, Christian; Matei, Mihaela; Canham, Steve; Panagiotopoulou, Maria; Demotes, Jacques; Thomassen, Gard; Blomberg, Niklas
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5519122

EOSC-Life WP4 Toolbox: Update of the categorisation system (version 3)

Author(s): Ohmann, Christian; Cano Abadía, Mónica; Bietrix, Florence; Boiten, Jan-Willem; Canham, Steve; Chiusano, Marie Luisa; Dastru, Walter; David, Romain; Laroquette, Arnaud; Longo, Dario; Mayrhofer, Michaela Theresia; Panagiotopoulou, Maria; Richard, Audrey
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5507324

EOSC-Life Summary of EOSC-Life Main Achievements and Impacts with Sustainability and Exploitation Plans

Author(s): Blomberg, Niklas; Schmidt-Tremmel, Friederike; Crockett, Sara
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8304575

Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Author(s): Crusoe, Michael R.; Abeln, Sanne; Iosup, Alexandru; Amstutz, Peter; Chilton, John; Tijanić, Nebojša; Ménager, Hervé; Soiland-Reyes, Stian; Gavrilovic, Bogdan; Goble, Carole
Published in: 2021
Publisher: arXiv.org
DOI: 10.48550/arxiv.2105.07028

EOSC-Life FAIRsharing webpage

Author(s): Sansone, Susanna-Assunta; Lister, Allyson; Thurston, Milo; Mirian, Hossein; Rocca-Serra, Philippe; Batista, Dominique; Granell, Ramon; Gailani, Prakhyat
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7019783

Life Science in EOSC: Summary of EOSC-Life impact and key results

Author(s): Blomberg, Niklas; Schmidt-Tremmel, Friederike; Ahern, Caitlin
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5179992

EOSC-Life Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures

Author(s): Canham, Steve; Ohmann, Christian; Thomassen, Gard; Matei, Mihaela; Demotes, Jacques; Panagiotopoulou, Maria
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4141619

EOSC-Life Guidance and policy on standards and tools to facilitate sharing and reuse of multimodal data (including imaging), cohort integration, and biosamples

Author(s): Boiten, Jan-Willem; Ohmann, Christian; Adeniran, Ayodeji; Canham, Steve; Cano Abadia, Monica; Chassang, Gauthier; Chiusano, Maria Luisa; David, Romain; Fratelli, Maddalena; Gribbon, Phil; Holub, Petr; Ludwig, Rebecca; Th. Mayrhofer, Michaela; Matei, Mihaela; Merchant, Arshiya; Panagiotopoulou, Maria; Pireddu, Luca; Richard, Audrey; Sanchez Pla, Alex; Schlünder, Irene; Tsamis, George; Wagener, Har
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4591011

EOSC-Life Access and User Management System for Life Science – the implementation and usage report

Author(s): Licehammer, Slavek; Linden, Mikael; Smith, Callum
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4559400

"Introduction to the ""Open Science and COVID-19"" webinar series"

Author(s): De Leo, Francesca
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5534897

EOSC-Life Access and User Management System for Life Science – the blueprint update

Author(s): Linden, Mikael; Bucik, Dominik Frantisek; Gormanns, Philipp; Haley, Natalie; Heikkinen, Jani; Holub, Petr; Kankaanpää, Pasi; Kouril, Daniel; Kuba, Martin; Licehammer, Slavek; Matyska, Ludek; Nyrönen, Tommi; Prochazka, Michal; Reihs, Robert; Romano, Paolo; Sanderson, Fiona; Shigaval, Athresh; Smith, Callum; Tedds, Jonathan
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4633190

Open Phytoliths Community Launch Event Presentations

Author(s): Karoune, Emma; García-Granero, Juan José; Lancelotti, Carla; Ruiz-Pérez, Javier; Kerfant, Celine; Dunseth, Zachary C; Musaubach, Maria Gabriela; Bates, Jennifer
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7090455

EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life

Author(s): Bietrix, Florence; Carazo, José Maria; Capella-Gutierrez, Salvador; Coppens, Frederik; Chiusano, Maria Luisa; David, Romain; Fernandez, Jose Maria; Fratelli, Maddalena; Heriche, Jean-Karim; Goble, Carole; Gribbon, Philip; Holub, Petr; P. Joosten, Robbie; Leo, Simone; Owen, Stuart; Parkinson, Helen; Pieruschka, Roland; Pireddu, Luca; Porcu, Luca; Raess, Michael; Rodriguez- Navas, Laura; Scherer, A
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4705078

ECRIN Clinical Research Metadata Schema Version 3.0 (November 2019)

Author(s): Canham, Steve
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.1312538

EOSC-Life Report about use and user satisfaction of the COVID-19 repository, including a maintenance and sustainability plan

Author(s): Contrino, Sergio; Felder, Gerd; Ohmann, Christian; Panagiotopoulou, Maria; Kichenassamy, Swarnalathaa; Gorianin, Sergei; Demotes, Jacques; Kouylekov, Milen; Thomassen, Gard
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7836812

EOSC-LIFE WP4 TOOLBOX: Toolbox for sharing of sensitive data - a concept description

Author(s): Boiten, Jan Willem; Ohmann, Christian; Adeniran, Ayodeji; Canham, Steve; Cano Abadia, Monica; Chassang, Gauthier; Chiusano, Maria Luisa; David, Romain; Fratelli, Maddalena; Gribbon, Phil; Holub, Petr; Ludwig, Rebecca; Mayrhofer, Michaela Th.; Matei, Mihaela; Merchant, Arshiya; Panagiotopoulou, Maria; Pireddu, Luca; Sanchez Pla, Alex; Schlünder, Irene; Tsamis, George; Wagener, Harald
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4483694

EOSC-Life Project plan for optional services and future cooperation with IDDO

Author(s): Panagiotopoulou, Maria; Rujano, Maria; Felder, Gerd; Contrino, Sergio; Ohmann, Christian; Kichenassamy, Swarnalathaa; Gorianin, Sergei; Demotes, Jacques; Kouylekov, Milen; Thomassen, Gard; Guerin, Philippe; Brack, Mathew
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8272763

EOSC-Life Data Management Plan

Author(s): Blomberg, Niklas; Sarntivijai, Sirarat; Mayrhofer, Michaela Th.
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4010442

EOSC-Life Report on identification and application of registries for FAIR data infrastructures

Author(s): Roos, Marco; da Salva Santos, Luiz Olavo Bonino
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8306174

EOSC-Life EOSC Cloud feasibility assessment for Demonstrators

Author(s): Gribbon, Philip; Parkinson, Helen; Witt, Gesa
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4010372

EOSC-Life Review of EOSC-Life training activities, their impact and potential adaptations

Author(s): Ludwig, Rebecca; Matser, Vera; Milano, Annalisa; Morgan, Sarah; López, Daniel Thomas; Deprez, Tim
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4562143

Umbrella Data Management Plans to integrate FAIR data : lessons from the ISIDORe and BY-COVID consortia for pandemic preparedness

Author(s): David, Romain; S. Richard, Audrey; 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
Published in: Data Science Journal, 2023, ISSN 1683-1470
Publisher: Ubiquity Press
DOI: 10.5281/zenodo.7516084

EOSC-Life Strategic Marketing and Stakeholder Mapping Report

Author(s): Ahern, Caitlin; Beatrix, Florence; Panagiotopoulou, Maria; Biziou, Laura
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4560453

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

Author(s): Canham, Steve
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4028900

A dataset for assessing phytolith data for implementation of the FAIR data principles

Author(s): Kerfant, Celine; Ruiz-Pérez, Javier; García-Granero, Juan José; Lancelotti, Carla; Madella, Marco; Karoune, Emma
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7215804

EOSC-Life Common Provenance Model

Author(s): Wittner, Rudolf; Mascia, Cecilia; Frexia, Francesca; Müller, Heimo; Geiger, Jörg; Exter, Katrina; Holub, Petr
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4705074

EOSC-Life Requirements for hosting/ distributing and access control for sensitive data

Author(s): Álvarez, Eva García; Ohmann, Christian; Saunders, Gary; Wagener, Harald; Colussi, Ilaria; Boiten, Jan-Willem; Panagiotopoulou, Maria; Cano Abadía, Mónica; David, Romain; Schluender, Irene; Holub, Petr; Mayrhofer, Michaela Th.
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7037444

Towards FAIR phytolith data: first steps down a long and winding road

Author(s): Karoune, Emma; Lancelotti, Carla; Ruiz-P��rez, Javier; Garc��a-Granero, Juanjo; Madella, Marco
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5336872

Non-repudiable provenance for clinical decision support systems

Author(s): Fairweather, Elliot; Wittner, Rudolf; Chapman, Martin; Holub, Petr; Curcin, Vasa
Published in: 2020
Publisher: Cornell University

Packaging research artefacts with RO-Crate

Author(s): Stian Soiland-Reyes; Peter Sefton; Mercè Crosas; Leyla Jael Castro; Frederik Coppens; José M. Fernández; Daniel Garijo; Björn Grüning; Marco La Rosa; Simone Leo; Eoghan Ó Carragáin; Marc Portier; Ana Trisovic; RO-Crate Community; Paul Groth; Carole Goble
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5146228

EOSC-Life WP4 Toolbox: Pilot study protocol for the evaluation of the categorisation system

Author(s): Ohmann, Christian; Canham, Steve; Boiten, Jan-Willem; Cano Abadía, Mónica; Chassang, Gautier; Chiusano, Maria Luisa; David, Romain; Mayrhofer, Michaela Theresia; Pireddu, Luca
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311114

EOSC-Life Access and User Management System for Life Science – the implementation and usage report

Author(s): Matyska, Ludek; Povey, Marcus; Frantisek Bucik, Dominik; Broncova, Jana; Licehammer, Slavek; Farrell, Gavin; Tedds, Jonathan; Romano, Paolo; Kankaanpää, Pasi; Linden, Mikael; Haley, Natalie; Gormanns, Philipp
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8144215

EOSC-Life EOSC FAIR services deployment for open calls

Author(s): Parkinson, Helen; Gribbon, Philip; Sarkans, Ugis; Witt, Gesa; Zaliani, Andrea; Kohler, Manfred; Swedlow, Jason; Burel, Jean-Marie; Swertz, Morris; van Enckevort, Esther; Holub, Petr; Massimi, Marzia; Matteoni, Rafaele; Maier, Holger; Hinttala, Reetta; Heikkinen, Anne; Gormanns, Philipp; Vasseur, Laurent; Leblanc, Sophie; Herault, Yann; Kontoyiannis, Dimitris; Chandras, Christina; Panou, Dimitra; L
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6208249

EOSC-Life Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes

Author(s): Panagiotopoulou, Maria; Yaïche, Sarhan; Michon, Amélie; Ohmann, Christian; Demotes, Jacques; Matei, Mihaela; Canham, Steve; Hjelle, Sigrun Margrethe; Klusek, Patrycja; Batuca, Joana; Schmid, Caecilia; Buoncervello, Maria; Toschi, Elena; Minghetti, Luisa; Chiusano, Maria Luisa; Vives Vilatersana, Adriana; Calvo I Orteu, María; Szabó, Zsolt; Součková, Lenka; Noskova, Kristyna; Kappala, Sharon;
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7148860

EOSC-Life Cloud implementation of exemplary workflows

Author(s): Rosato, Antonio; Hériché, Jean-Karim; Serrano-Solano, Beatriz; Grüning, Björn; Pireddu, Luca; Goble, Carole
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4010401

Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory

Author(s): Goble, Carole; Soiland-Reyes, Stian; Bacall, Finn; Owen, Stuart; Williams, Alan; Eguinoa, Ignacio; Droesbeke, Bert; Leo, Simone; Pireddu, Luca; Rodríguez-Navas, Laura; Fernández, José Mª; Capella-Gutierrez, Salvador; Ménager, Hervé; Grüning, Björn; Serrano-Solano, Beatriz; Ewels, Philip; Coppens, Frederik
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4605654

EOSC-Life Data mobilisation summary

Author(s): Rahman, Nadim; Ventouratou, Marianna
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7097237

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers

Author(s): Zullino, Sara; Paglialonga, Alessandro; Dastrù, Walter; Longo, Dario Livio; Aime, Silvio
Published in: 2021
Publisher: Cornell University

EOSC - a tool for enabling Open Science in Europe

Author(s): Owen Appleton; Ari Asmi; Ian Bird; Ron Dekker; Niklas Blomberg; Rudolf Dimper; Tiziana Ferrari; Annabel Grant; Sarah Jones; Natalia Manola; Andreas Petzold; Najla Rettberg; Dale Robertson; Ville Tenhunen; Debora Testi; Mark van de Sanden
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4044010

Event series: Open Science and Covid-19. Working together to fight the pandemic

Author(s): De Leo, Francesca; Lazzeri, Emma; Le Pera, Loredana; Pavone, Gina; Via, Allegra
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4147034

Final release: COVID-19 guidelines

Author(s): Research Data Alliance
Published in: 2020
Publisher: Zenodo
DOI: 10.15497/rda00052

EOSC-Life Initial EOSC-LS Cloud Observatory Report

Author(s): Newhouse, Steven; Wagener, Harald; González Ferrero, Montserrat; Fano-Bilbao, Oihane; Wildish, Tony; Dieckmann, Marius; Niewielska, Ania; Kapoor, Shubham; Nyrönen, Tommi
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4010420

RO-Crate Metadata Specification 1.1.1

Author(s): Peter Sefton; Eoghan Ó Carragáin; Stian Soiland-Reyes; Oscar Corcho; Daniel Garijo; Raul Palma; Frederik Coppens; Carole Goble; José María Fernández; Kyle Chard; Jose Manuel Gomez-Perez; Michael R Crusoe; Ignacio Eguinoa; Nick Juty; Kristi Holmes; Jason A. Clark; Salvador Capella-Gutierrez; Alasdair J. G. Gray; Stuart Owen; Alan R. Williams; Giacomo Tartari; Finn Bacall; Thomas Thelen; Hervé
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.3406497

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

Author(s): 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
Published in: https://hal.inrae.fr/hal-02570809, 2019
Publisher: INRA
DOI: 10.15454/1.5572412770331912E12

EOSC-Life Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures - v2

Author(s): Canham, Steve; Ohmann, Christian; Thomassen, Gard; Matei, Mihaela; Demotes, Jacques; Panagiotopoulou, Maria
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4341385

ECRIN Metadata Schemas for Clinical Research Data Objects Version 5.0 (October 2020)

Author(s): Canham, Steve
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4133889

EOSC-Life Publication of generic guidelines for the organization of topic-specific Open Calls

Author(s): Haley, Natalie; Leitner, Frauke; Bischof, Johanna; Audergon, Pauline
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4048442

Open Science Strength and its cooperation method in the current pandemic context

Author(s): Lazzeri, Emma
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3955640

Open Source Secure Data Infrastructure and Processes for Data Visiting

Author(s): Weise, Martin; Rauber, Andreas
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4632903

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: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5727730

Sensitive Data IG RDA17 Session Report

Author(s): Akmon, Dharma; Burton, Nichola; David, Romain; Davidson, Sarah; McEachern, Steven; Michalewicz, Aleksandra; Pillai, Priyanka; Rb-Silva, Rita; Spreadborough, Kristal; Stevens, Frankie
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5002793

EOSC-Life Implementation of a mechanism for publishing and sharing workflows across instances of the environment

Author(s): Goble, Carole; Soiland-Reyes, Stian; Bacall, Finn; Owen, Stuart; Pireddu, Luca; Leo, Simone
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7886545

EOSC-Life Review of Effectiveness and Impact of Outreach and Stakeholder Engagement

Author(s): Crockett, Sara; Panagiotopoulou, Maria; Esdaile, Martina; Ludwig, Rebecca; Gurwitz, Kim; Saunders, Gary
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8276753

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

Author(s): Ramirez-Aportela, Erney; Maluenda, David; Fonseca, Yunior C.; Conesa, Pablo; Marabini, Roberto; Heymann, J. Bernard; Carazo, Jose Maria; Sorzano, Carlos Oscar S.
Published in: BioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.12.069831

EOSC-Life Access and user management system for life science – the blueprint

EOSC-Life FAIR Requirements Document

Author(s): Perseil, Isabelle; Sansone, Susanna-Assunta; McQuilton, Peter; Dumontier, Michel; Roos, Marco; Bonino, Luiz; Wittner, Rudolf; Holub, Petr; Geiger, Jörg
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3693883

ESFRI cluster projects - Position papers on expectations and planned contributions to the EOSC

Author(s): Gotz, Andy; Petzold, Andreas; Asmi, Ari; Blomberg, Niklas; Lamanna, Giovanni; Dekker, Ron
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3675081

EOSC-Life Final report of analysis of the training needs of different EOSC-Life users

Author(s): Matser, Vera; Ludwig, Rebecca; Kolodkin, Alexey; Milano, Annalisa; Keppler, Antje; Brooksbank, Cath; Von Gelder, Celia; Amaro, Claudia Alen; Leitner, Frauke; Rustici, Gabriella; Westerhoff, Hans; Heriche, Jean-Karim; EXTER, Katrina; Haley, Natalie; Kankaanpää, Pasi; Scholtens, Salome; Morgan, Sarah
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3692068

Towards a reconstructive methodology for building a provenance metamodel that fits the complex bioinformatics pipelines

Author(s): Isabelle Perseil; Petr Holub
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3362412

usegalaxy.be

Author(s): Coppens, Frederik
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6607021

FAIR Computational Workflows

Author(s): Goble, Carole; Cohen-Boulakia, Sarah; Schober, Daniel; Peters, Kristian; Soiland-Reyes, Stian; Garijo, Daniel; Gil, Yolanda; Crusoe, Michael R.
Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3528076

Open Science in Archaeobotany - The FAIR Phytoliths Project

Author(s): Kerfant, Celine; Karoune, Emma; Lancelotti, Carla; Ruiz-P��rez, Javier; Garc��a-Granero, Juan Jos��; Madella, Marco
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6335633

Machine actionable metadata models

Author(s): Batista, Dominique; Gonzalez-Beltran, Alejandra; Sansone, Susanna-Assunta; Rocca-Serra, Philippe
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5596465

ECRIN Metadata Schemas for Clinical Research, Version 8 (September 2023)

Author(s): Steve Canham
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8368709

EOSC-Life Access and User Management System for Life Science – the blueprint update

Author(s): Linden, Mikael; Bucik, Dominik Frantisek; Gormanns, Philipp; Haley, Natalie; Heikkinen, Jani; Holub, Petr; Kankaanpää, Pasi; Kouril, Daniel; Kuba, Martin; Licehammer, Slavek; Matyska, Ludek; Nyrönen, Tommi; Prochazka, Michal; Reihs, Robert; Romano, Paolo; Shigaval, Athresh; Povey, Marcus; Tedds, Jonathan
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6782892

EOSC-Life WP4 Toolbox: Update of the categorisation system

Multitarget Virtual Screening for Drug Repurposing in COVID19

Author(s): Sorzano, carlos oscar; Crisman, Enrique; Carazo, Jose Maria; leon, rafael
Published in: 2020
Publisher: ChemXriv
DOI: 10.26434/chemrxiv.12652997.v2

EOSC-Life Report on the work of the initial demonstrators

Author(s): Leitner, Frauke; Carazo, Jose Maria; Bischof, Johanna; Haley, Natalie; Audergon, Pauline; Sorzano, Carlos Oscar; del Cano, Laura; Conesa, Pablo; Cox, Cymon J.; De Moro, Gianluca; Erwan, Corre; Exter, Katrina; Le Corguillé, Gildas; Dallet, Romain; Gueguen, Lorraine; Heriche, Jean-Karim; Serrano, Beatriz; Sun, Yi; Burel, Jean-Marie; Zullino, Sara; Longo, Dario Livio; Pommier, Cyril; Hallab, Asis; E
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4817723

EOSC-Life FAIR assistance

Author(s): Sansone, Susanna-Assunta; Lister, Allyson; Thurston, Milo; Rocca-Serra, Philippe; Batista, Dominique; Granell, Ramon; Gailani, Prakhyat; Dumontier, Michel
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8264604

EOSC-Life Final EOSC-LS Cloud Observatory Report

Author(s): Newhouse, Steven; Wagener, Harald; Dieckmann, Marius; Niewielska, Ania; Clark-Casey, Justin; Insua, Santiago
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6555209

Building a FAIR image data ecosystem for microscopy communities

Author(s): Kemmer, Isabel; Keppler, Antje; Serrano-Solano, Beatriz; Rybina, Arina; Özdemir, Bugra; Bischof, Johanna; El Ghadraoui, Ayoub; Eriksson, John E.; Mathur, Aastha
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7788898

EOSC-Life Report on the work of the Open Call Projects

Author(s): Rybina, Arina; Audergon, Pauline; Pfander, Claudia
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8263074

EOSC-Life Common provenance model for processing biological material, data generation and computational workflows

Author(s): Wittner, Rudolf; Geiger, Jörg; Müller, Heimo; Frexia, Francesca; Mascia, Cecilia; Exter, Katrina; Cancio, Ibon; Holub, Petr
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8279525

ESFRI Science Clusters Position Statement on Expectations and Long-Term Commitment in Open Science

Author(s): Giovanni Lamanna; Ian Bird; Andreas Petzold; Ari Asmi; Magdalena Brus; Niklas Blomberg; Michael Räß; Rudolf Dimper; Andrew Gotz; Ron Dekker
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4892245

EOSC FAIR services deployment for open calls

Author(s): Parkinson H. et al.
Published in: 2022, Issue 20, 2022
Publisher: CNR

EOSC-Life Final report on EOSC-Life training activities and their impact

Author(s): Ludwig, Rebecca; Duquenne, Lauranne; Gurwitz, Kim; Swan, Anna; Thomas Lopez, Daniel; Lloret Llinares, Marta; Delgado, Claudia
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8083413

EOSC-Life EOSC repository deployment for project demonstrators

Author(s): Parkinson, Helen; Gribbon, Philip; Sarkans, Ugis; Witt, Gesa; Zaliani, Andrea; Kohler, Manfred; Swedlow, Jason; Burel, Jean-Marie; Swertz, Morris; van Enckevort, Esther; Holub, Petr; Massimi, Marzia; Matteonie, Rafaele; Maier, Holger; Hinttala, Reetta; Heikkinen, Anne; Gormanns, Philipp; del Cano, Laura; Vasseur, Laurent; Leblanc, Sophie; Herault, Yann; Kontoyiannis, Dimitris; Chandras, Christina;
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4432029

EOSC-Life Enhanced COVID-19 Portal and data mobilisation reporting

Author(s): Cochrane, Guy; Ventouratou, Marianna
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5642935

EOSC-Life Report on requirements for regulatory compliance of sensitive health data and biological and medical research data

Author(s): Battaglia, Serena; Mayrhofer, Michaela T.; Matei, Mihaela; Boiten, Jan-Willem; Ohmann, Christian; Schlünder, Irene; Adeniran, Ayodeji
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3820389

Open Phytolith Publishing Guidelines

Author(s): Karoune, Emma; Barboni, Doris; Bates, Jennifer; Dabengwa, Abraham; Dunseth, Zachary C; García-Granero, Juan José; Kerfant, Celine; Lancelotti, Carla; Madella, Marco; Musaubach, Maria Gabriela; Ruiz-Pérez, Javier
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6803489

EOSC-Life A common environment that can run cross-RIs workflows

Author(s): Rosato, Antonio; Hériché, Jean-Karim
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7217293

EOSC-Life WP4 Toolbox: Categorisation system for resources to be referenced in the toolbox for sharing of sensitive data

Author(s): Ohmann, Christian; Canham, Steve; Boiten, Jan-Willem; Cano Abadía, Mónica; Chassang, Gautier; Chiusano, Marie Luisa; David, Romain; Mayrhofer, Michaela Theresia; Pireddu, Luca
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4311094

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

Author(s): Bray, Simon A.; Senapathi, Tharindu; Barnett, Christopher B.; Grüning, Björn A.
Published in: BioRxiv, 2020
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2020.05.08.084780

10 Simple Rules for making a software tool workflow-ready

Author(s): Brack, Paul; Crowther, Peter; Soiland-Reyes, Stian; Owen, Stuart; Lowe, Douglas; Williams, Alan R; Groom, Quentin; Dillen, Mathias; Coppens, Frederik; Grüning, Björn; Eguinoa, Ignacio; Ewels, Philip; Goble, Carole
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5636487

EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version

Author(s): Bietrix, Florence; Carazo, José Maria; Capella-Gutierrez, Salvador; Coppens, Frederik; Chiusano, Maria Luisa; David, Romain; Fernandez, Jose Maria; Fratelli, Maddalena; Heriche, Jean-Karim; Goble, Carole; Gribbon, Philip; Holub, Petr; P. Joosten, Robbie; Leo, Simone; Owen, Stuart; Parkinson, Helen; Pieruschka, Roland; Pireddu, Luca; Porcu, Luca; Raess, Michael; Rodriguez-Navas, Laura; Scherer, An
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7137743

EOSC-Life Report about technical implementation and validation of the COVID-19 portal

Author(s): Canham, Steve; Gorianin, Sergey; Kouylekov, Milen; Panagiotopoulou, Maria; Ohmann, Christian; Kichenassamy, Swarnalathaa; Thomassen, Gard; Fugelli, Pål; Demotes, Jacques
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6555207

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

Author(s): Jose Luis Vilas, Hemant D. Tagare, Javier Vargas, Jose Maria Carazo, Carlos Oscar S. Sorzano
Published in: Nature Communications, Issue 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-13742-w

Automated Determination of Nuclear Magnetic Resonance Chemical Shift Perturbations in Ligand Screening Experiments: The PICASSO Web Server.

Author(s): Vincenzo Laveglia; Andrea Giachetti; Linda Cerofolini; Kevin Haubrich; Marco Fragai; Alessio Ciulli; Antonio Rosato
Published in: Journal of Chemical Information and Modeling, 2021, Page(s) 5726–5733, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.1c00871

DrugComb: an integrative cancer drug combination data portal.

Author(s): Zagidullin, Bulat; Aldahdooh, Jehad; Zheng, Shuyu; Wang, Wenyu; Wang, Yinyin; Saad, Joseph; Malyutina, Alina; Jafari, Mohieddin; Tanoli, Ziaurrehman; Pessia, Alberto; Tang, Jing
Published in: Nucleic Acids Research, 2019, Page(s) W43-W51, ISSN 1362-4962
Publisher: Oxford University Press
DOI: 10.1101/560227

Privacy Risks of Whole-Slide Image Sharing in Digital Pathology

Author(s): Petr Holub; Heimo Müller; Tomáš Bíl; Luca Pireddu; Markus Plass; Fabian Prasser; Irene Schlünder; Kurt Zatloukal; Rudolf Nenutil; Tomáš Brázdil
Published in: Nature Communications, 2023, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.21203/rs.3.rs-1593472/v1

Importing genetically altered animals: ensuring quality.

Author(s): Marie-Christine Birling; Martin Fray; Petr Kasparek; J. Kopkanova; M. Massimi; R. Matteoni; Lluis Montoliu; Lauryl M J Nutter; Marcello Raspa; Jan Rozman; Edward Ryder; Edward Ryder; Ferdinando Scavizzi; V. Voikar; Sara Wells; Guillaume Pavlovic; Lydia Teboul
Published in: Mammalian Genome, Issue 09388990, 2022, Page(s) 100-107, ISSN 0938-8990
Publisher: Springer Verlag
DOI: 10.1007/s00335-021-09908-x

FAIRness Literacy: The Achilles’ Heel of Applying FAIR Principles

Author(s): 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
Published in: Data Science Journal, Issue 19, 2020, ISSN 1683-1470
Publisher: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2020-032

Accessible and reproducible mass spectrometry imaging data analysis in Galaxy

Author(s): Melanie Christine Föll, Lennart Moritz, Thomas Wollmann, Maren Nicole Stillger, Niklas Vockert, Martin Werner, Peter Bronsert, Karl Rohr, Björn Andreas Grüning, Oliver Schilling
Published in: GigaScience, Issue 8/12, 2019, ISSN 2047-217X
Publisher: Oxford University Press
DOI: 10.1093/gigascience/giz143

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

Author(s): Caracciolo, Caterina; Aubin, Sophie; Jonquet, Clement; Amdouni, Emna; David, Romain; Garcia, Leyla; Whitehead, Brandon; Roussey, Catherine; Stellato, Armando; Villa, Ferdinando
Published in: "CODATA Data Science Journal, Committee on Data for Science and Technology (CODATA), 2020, 19 (1), ⟨10.5334/dsj-2020-047⟩", Issue 3, 2020, ISSN 1683-1470
Publisher: Committee on Data for Science and Technology (CODATA) International Council for Science (ICSU)
DOI: 10.5334/dsj-2020-047

Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release

Author(s): Domenico Rizzo; Linda Cerofolini; Anna Pérez-Ràfols; Stefano Giuntini; Fabio Baroni; Enrico Ravera; Claudio Luchinat; Marco Fragai
Published in: Analytical Chemistry, 2021, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.1c01850

Learning to Identify Physiological and Adventitious Metal-Binding Sites in the Three-Dimensional Structures of Proteins by Following the Hints of a Deep Neural Network

Author(s): Vincenzo Laveglia; Andrea Giachetti; Davide Sala; Claudia Andreini; Antonio Rosato
Published in: Journal of Chemical Information and Modeling, Issue 62, 2022, Page(s) 2951, ISSN 1549-9596
Publisher: American Chemical Society
DOI: 10.1021/acs.jcim.2c00522

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service.

Author(s): Marco Antonio Tangaro; Pietro Mandreoli; Pietro Mandreoli; Matteo Chiara; Matteo Chiara; Giacinto Donvito; Marica Antonacci; Antonio Parisi; Angelica Bianco; Angelo Romano; Daniela Bianchi; Davide Cangelosi; Paolo Uva; Ivan Molineris; Vladimir Nosi; Raffaele A. Calogero; Luca Alessandrì; Elena Pedrini; Marina Mordenti; Emanuele Bonetti; Luca Sangiorgi; Graziano Pesole; Graziano Pesole; Federico Z
Published in: BMC Bioinformatics, Vol 22, Iss S15, Pp 1-21 (2021), Issue 16, 2021, ISSN 1471-2105
Publisher: BioMed Central
DOI: 10.1186/s12859-021-04401-3

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

Author(s): 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
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-019-0184-5

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

Author(s): Ziaurrehman Tanoli, Umair Seemab, Andreas Scherer, Krister Wennerberg, Jing Tang, Markus Vähä-Koskela
Published in: Briefings in Bioinformatics, 2020, ISSN 1477-4054
Publisher: Oxford University Press
DOI: 10.1093/bib/bbaa003

GXP: Analyze and Plot Plant Omics Data in Web Browsers

Author(s): Constantin Eiteneuer; David Velasco; Joseph Atemia; Dan Wang; Rainer Schwacke; Vanessa Wahl; Andrea Schrader; Julia J. Reimer; Sven Fahrner; Roland Pieruschka; Ulrich Schurr; Björn Usadel; Asis Hallab
Published in: Plants, Issue 11, 2022, Page(s) 745, ISSN 2223-7747
Publisher: MDPI Journals
DOI: 10.3390/plants11060745

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

Author(s): Matthias Obst, Katrina Exter, A. Louise Allcock, Christos Arvanitidis, Alizz Axberg, Maria Bustamante, Ibon Cancio, Diego Carreira-Flores, Eva Chatzinikolaou, Giorgos Chatzigeorgiou, Nathan Chrismas, Melody S. Clark, Thierry Comtet, Thanos Dailianis, Neil Davies, Klaas Deneudt, Oihane Diaz de Cerio, Ana Fortič, Vasilis Gerovasileiou, Pascal I. Hablützel, Kleoniki Keklikoglou, Georgios Kotoulas,
Published in: Frontiers in Marine Science, Issue 7, 2020, ISSN 2296-7745
Publisher: Frontiers Media
DOI: 10.3389/fmars.2020.572680

An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data

Author(s): Romain David; Christian Ohmann; Jan-Willem Boiten; Mónica Cano Abadía; Florence Bietrix; Steve Canham; Maria Luisa Chiusano; Walter Dastrù; Arnaud Laroquette; Dario Longo; Michaela Th. Mayrhofer; Maria Panagiotopoulou; Audrey S. Richard; Sergey Goryanin; Pablo Emilio Verde
Published in: Scientific Reports, Issue 12, 2022, Page(s) 20989, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-022-25278-z

Experiment design driven FAIRification of omics data matrices, an exemplar

Author(s): Philippe Rocca-Serra, Susanna-Assunta Sansone
Published in: Scientific Data, Issue 6/1, 2019, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1038/s41597-019-0286-0

Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines

Author(s): Brian Pickering; Timea Biro; Claire C. Austin; Alexander Bernier; Louise Bezuidenhout; Carlos Casorran; Francis P. Crawley; Romain David; Claudia Engelhardt; Geta Mitrea; Ingvill C. Mochmann; Rajini Nagrani; Mary O'Brien-Uhlmansiek; Simon Parker; Minglu Wang; Leyla Jael Castro; Zoe Cournia; Kheeran Dharmawardena; Gayo Diallo; Ingrid Dillo; Alejandra Gonzalez-Beltran; Anupama Gururaj; Sridhar Gutam
Published in: Open Research Europe, Issue 15, 2021, ISSN 2732-5121
Publisher: European Commission
DOI: 10.12688/openreseurope.13369.1

Improvements on marker-free images alignment for electron tomography

Author(s): C.O.S. Sorzano, F. de Isidro-Gómez, E. Fernández-Giménez, D. Herreros, S. Marco, J.M. Carazo, C. Messaoudi
Published in: Journal of Structural Biology: X, Issue 4, 2020, Page(s) 100037, ISSN 2590-1524
Publisher: ELSEVIER
DOI: 10.1016/j.yjsbx.2020.100037

Cryo-EM density maps adjustment for subtraction, consensus and sharpening.

Author(s): E. Fernández-Giménez; María Jesús Martínez; Rubén J. Sánchez-García; Roberto Marabini; Erney Ramírez-Aportela; Pablo Conesa; José María Carazo; Carlos Oscar S. Sorzano
Published in: Journal of Structural Biology, Issue 15, 2021, ISSN 1047-8477
Publisher: Academic Press
DOI: 10.1016/j.jsb.2021.107780

XNAT-PIC: Extending XNAT to Preclinical Imaging Centers

Author(s): Sara Zullino; Alessandro Paglialonga; Walter Dastrù; Dario Livio Longo; Silvio Aime
Published in: J Digit Imaging, 2022, ISSN 1618-727X
Publisher: Springer Nature
DOI: 10.1007/s10278-022-00612-z

Advances in Xmipp for Cryo-Electron Microscopy: From Xmipp to Scipion.

Author(s): David Strelak; A. Jiménez-Moreno; José Luis Vilas; Erney Ramírez-Aportela; Rubén J. Sánchez-García; David Maluenda; Javier Vargas; David Herreros; E. Fernández-Giménez; Federico P. de Isidro-Gómez; Jan Horáček; David Myška; Martin Horacek; Pablo Conesa; Yunior C. Fonseca-Reyna; Jorge Jiménez; Marta Martínez; Mohamad Harastani; Slavica Jonic; Jiri Filipovic; Roberto Marabini; José Ma
Published in: Volume 26, Issue 2, 2021, ISSN 1420-3049
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/molecules26206224

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

Author(s): David Střelák, Jiří Filipovič, Amaya Jiménez-Moreno, Jose Carazo, Carlos Sánchez Sorzano
Published in: Electronics, Issue 9/6, 2020, Page(s) 1040, ISSN 2079-9292
Publisher: MDPI
DOI: 10.3390/electronics9061040

Expanding the Galaxy's reference data

Author(s): Nagampalli Vijaykrishna; Jayadev Joshi; Nate Coraor; Jennifer Hillman-Jackson; Dave Bouvier; Marius van den Beek; Ignacio Eguinoa; Frederik Coppens; Sergey Golitsynskiy; Michał Stolarczyk; Nathan C. Sheffield; Simon Gladman; Gianmauro Cuccuru; Björn Grüning; Nicola Soranzo; Helena Rasche; Bradley W. Langhorst; Matthias Bernt; Daniel Fornika; David Anderson de Lima Morais; Michel Barrette; Peter
Published in: urn:issn:2635-0041, Issue 4, 2022, ISSN 2635-0041
Publisher: Oxford University Press
DOI: 10.1101/2020.10.09.327114

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

Author(s): Daniel Jacob, Romain David, Sophie Aubin, Yves Gibon
Published in: GigaScience, Issue 9/12, 2020, ISSN 2047-217X
Publisher: GigaScience, BioMed Central
DOI: 10.1093/gigascience/giaa144

DeepEMhancer: a deep learning solution for cryo-EM volume post-processing

Author(s): Rubén J. Sánchez-García; Rubén J. Sánchez-García; Josué Gómez-Blanco; Josué Gómez-Blanco; Ana Maria Cuervo; José María Carazo; Carlos Oscar S. Sorzano; Javier Vargas; Javier Vargas
Published in: Communications Biology, Issue 10, 2021, ISSN 2399-3642
Publisher: Nature Portfolio
DOI: 10.1101/2020.06.12.148296

Ten simple rules for making a software tool workflow-ready

Author(s): Paul Brack, Peter Crowther, Stian Soiland-Reyes, Stuart Owen, Douglas Lowe, Alan R. Williams, Quentin Groom, Mathias Dillen, Frederik Coppens, Björn Grüning, Ignacio Eguinoa, Philip Ewels, Carole Goble
Published in: PLOS Computational Biology, 2022, ISSN 1553-7358
Publisher: PLOS
DOI: 10.1371/journal.pcbi.1009823

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

Author(s): Abulikemu Abudukelimu, Matteo Barberis, Frank Redegeld, Nilgun Sahin, Raju P. Sharma, Hans V. Westerhoff
Published in: Frontiers in Immunology, Issue 10, 2020, ISSN 1664-3224
Publisher: Frontiers
DOI: 10.3389/fimmu.2019.03091

A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge

Author(s): Miroslav Hruska; Dusan Holub
Published in: International Journal of Mass Spectrometry, Issue 3, 2021, ISSN 1387-3806
Publisher: Elsevier BV
DOI: 10.1016/j.ijms.2021.116723

FAIRsharing as a community approach to standards, repositories and policies

Author(s): Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson L. Lister, Milo Thurston
Published in: Nature Biotechnology, Issue 37/4, 2019, Page(s) 358-367, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-019-0080-8

Perspectives on automated composition of workflows in the life sciences

Author(s): Anna-Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J. O. Baker; A. Amor; Salvador Capella-Gutierrez; Paulos Charonyktakis; Michael R. Crusoe; Yolanda Gil; Carole Goble; Timothy J. Griffin; Paul Groth; Hans Ienasescu; Pratik D. Jagtap; Matúš Kalaš; Vedran Kasalica; Alireza Khanteymoori; Tobias Kuhn; Hailiang Mei; Hervé Ménager
Published in: F1000Research, Issue 10, 2021, Page(s) 897, ISSN 2046-1402
Publisher: F1000 Research Ltd.
DOI: 10.12688/f1000research.54159.1

Toward Human–AI Interfaces to Support Explainability and Causability in Medical AI

Author(s): Andreas Holzinger; Heimo Müller
Published in: Computer, Issue 19, 2021, ISSN 0018-9162
Publisher: Institute of Electrical and Electronics Engineers
DOI: 10.1109/mc.2021.3092610

3DBionotes COVID-19 edition

Author(s): Jose Ramon Macias, Ruben Sanchez-Garcia, Pablo Conesa, Erney Ramirez-Aportela, Marta Martinez Gonzalez, Carlos Wert-Carvajal, Alberto M Parra-Perez, Joan Segura Mora, Sam Horrell, Andrea Thorn, Carlos O S Sorzano, Jose Maria Carazo
Published in: Bioinformatics, 2021, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/btab397

Gold-Based Metal Drugs as Inhibitors of Coronavirus Proteins: The Inhibition of SARS-CoV-2 Main Protease by Auranofin and Its Analogs

Author(s): Lara Massai; Deborah Grifagni; Alessia De Santis; Andrea Geri; Francesca Cantini; Vito Calderone; Lucia Banci; Luigi Messori
Published in: Biomolecules, Issue Volume 12 Issue 11, 2022, Page(s) 1675, ISSN 2218-273X
Publisher: MDPI
DOI: 10.3390/biom12111675

Mouse Mutants of Gpr37 and Gpr37l1 Receptor Genes: Disease Modeling Applications

Author(s): Marzia Massimi; Chiara Di Pietro; Gina La Sala; Rafaele Matteoni
Published in: International Journal of Molecular Sciences, Issue 23, 2022, Page(s) 4288, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms23084288

The Image Data Explorer: interactive exploration of image-derived data

Author(s): Coralie Muller; Beatriz Serrano-Solano; Yi Sun; Christian Tischer; Jean-Karim Hériché
Published in: PLoS ONE, Issue 1, 2022, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1101/2022.04.27.489647

FAIR Computational Workflows

Author(s): Carole Goble, Sarah Cohen-Boulakia, Stian Soiland-Reyes, Daniel Garijo, Yolanda Gil, Michael R. Crusoe, Kristian Peters, Daniel Schober
Published in: Data Intelligence, Issue 2/1-2, 2020, Page(s) 108-121, ISSN 2641-435X
Publisher: MIT Press
DOI: 10.1162/dint_a_00033

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures

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Published in: IUCrJ, Issue 7/6, 2020, Page(s) 1059-1069, ISSN 2052-2525
Publisher: International Union of Crystallography
DOI: 10.1107/s2052252520012725

Bridging the Gap Between Remote Sensing and Plant Phenotyping-Challenges and Opportunities for the Next Generation of Sustainable Agriculture.

Author(s): Miriam Machwitz; Roland Pieruschka; Katja Berger; Martin Schlerf; Helge Aasen; Sven Fahrner; José A. Jiménez-Berni; Frédéric Baret; Uwe Rascher
Published in: Frontiers in Plant Science, Issue 12, 2021, Page(s) 749374, ISSN 1664-462X
Publisher: Frontiers Media S. A.
DOI: 10.3929/ethz-b-000515491

Evaluation of an integrative Bayesian peptide detection approach on a combinatorial peptide library

Author(s): Miroslav Hruska; Dusan Holub
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Publisher: IM Publications
DOI: 10.1177/14690667211066725

Measurement of local resolution in electron tomography

Author(s): J.L. Vilas, J. Oton, C. Messaoudi, R. Melero, P. Conesa, E. Ramirez-Aportela, J. Mota, M. Martinez, A. Jimenez, R. Marabini, J.M. Carazo, J. Vargas, C.O.S. Sorzano
Published in: Journal of Structural Biology: X, Issue 4, 2020, Page(s) 100016, ISSN 2590-1524
Publisher: Elsevier
DOI: 10.1016/j.yjsbx.2019.100016

INFRAFRONTIER Supports Targeting Cancer with Animal Models

Author(s): F. Song; A. Ali Khan; R. Matteoni; S. Fessele; M. Raess; M. Hrabe de Angelis
Published in: European Association for Cancer Research (EACR) 2021 Virtual Congress, 9-12 June 2021, 2021
Publisher: EACR

Packaging and describing Data Collections with RO-Crate

Author(s): Goble, Carole; Soiland-Reyes, Stian; Corcho, Oscar
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4916167

Data sharing in the Covid-19 era: challenges and opportunities for Italy. The contribution of ELIXIR

Author(s): Pesole, Graziano
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3955997

RO-Crate: Describing and packaging FAIR Research Objects

Author(s): Soiland-Reyes, Stian; Goble, Carole
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4633654

Capturing workflow life cycle with RO-Crate

Author(s): Soiland-Reyes, Stian
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4926087

Using Repositories Workshop

Author(s): Karoune, Emma; Lancelotti, Carla; Bates, Jennifer; Dabengwa, Abraham; Dunseth, Zachary; García-Granero, Juan José; Ge, Yong; Kerfant, Celine; Madella, Marco; Musaubach, Maria Gabriela; Ruiz-Pérez, Javier
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7717229

Progress towards open science in phytolith research: International Committee on Open Phytolith Science (ICOPS)

Author(s): Karoune, Emma; Lancelotti, Carla; Bates, Jennifer; Dabengwa, Abraham; Dunseth, Zachary; García-Granero, Juan José; Ge, Yong; Kerfant, Celine; Madella, Marco; Musaubach, Maria Gabriela; Ruiz-Pérez, Javier; Barboni, Doris
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8287352

Thematic Discovery Marketplaces for the European Open Science Cloud

Author(s): Appleton, Owen; Andreas, Petzold; Graf, Kay; Goble, Carole; Fischer, Frank; Richter, Tobias; Willems, Marieke
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4277601

EOSC-Life pilot study on the intercalibration of a categorisation system for FAIRer digital objects related to sensitive data in the life sciences

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Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5729436

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Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4011999

Multilingual Data Challenges in Professionalizing Data Stewardship worldwide

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Publisher: Zenodo
DOI: 10.5281/zenodo.6587897

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Author(s): 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
Published in: 4th Provenance Week 2020, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.3901011

Removing Barriers to Reproducible Research in Archaeology

Author(s): Plomp, Esther; Karoune, Emma
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6784277

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Author(s): Coppens, Frederik
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4326600

Towards a reconstructive methodology for building a provenance metamodel that fits the complex bioinformatics pipelines

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Published in: 2019
Publisher: Zenodo
DOI: 10.5281/zenodo.3362411

Cookbook pour dictionnaire de données pour l'interopération des données et logiciels de recherche à l'échelle globale

Author(s): David, Romain; Bouveret, Laurent; Coché, Lorraine; Corrêa, Pedro Pizzigatti; Edmunds, Rorie; Filippone, Claudia; Heredia, Ana; Jung, Jean-Luc; Le Berre, Iwan; Le Bras, Yvan; Lerigoleur, Emilie; Mabile, Laurence; Machicao, Jeaneth; Madon, Bénédicte; Murayama, Yasuhiro; O'Brien, Margaret; Osawa, Takeshi; Raoul, Hervé; Richard, Audrey; Santos, Solange; Specht, Alison; Stall, Shelley; Stepanyan,
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5749695

Train-the-Trainer | Integration of the sex and gender dimension in life sciences research - slides

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Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8183682

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

Author(s): , Ramon; , Delphine; , Allyson; , Milo; , Susanna-Assunta
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7064636

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Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7853116

Data dictionary cookbook for research data and software interoperability at global scale

Author(s): David, Romain; Bouveret, Laurent; Coché, Lorraine; Corrêa, Pedro Pizzigatti; Edmunds, Rorie; Heredia, Ana; Jung, Jean-Luc; Kondo, Yasuhisa; Le Berre, Iwan; Le Bras, Yvan; Lerigoleur, Emilie; Mabile, Laurence; Machicao, Jeaneth; Madon, Bénédicte; Murayama, Yasuhiro; O'Brien, Margaret; Osawa, Takeshi; Raoul, Hervé; Richard, Audrey; Santos, Solange; Specht, Alison; Stall, Shelley; Stepanyan, Dia
Published in: https://www.rd-alliance.org/plenaries/rda-17th-plenary-meeting-edinburgh-virtual, 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4683066

FAIR Data Stewardship Training & Capacity Building

Author(s): Celia W.G. van Gelder
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8031710

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Author(s): Soiland-Reyes, Stian
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5007432

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

Author(s): David, Romain; Richard, Audrey; Stepanyann, Diana; Versteeg, Krista; Mineau-Cesari, Jonathan; Mistou, Michel-Yves; Mabile, Laurence; Raoul, Hervé
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4293611

Communicating phytolith data transparently and reproducibility using the FAIR data principles

Author(s): Karoune, Emma; Lancelotti, Carla; Ruiz-Pérez, Javier; García-Granero, Juan José; Madella, Marco; Kerfant, Celine
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7813203

Livro de receitas de dicionário de dados para dados de pesquisa e interoperabilidade de software em escala global

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Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5021359

Building an interoperable Genomic Data Infrastructure

Author(s): Coppens, Frederik
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6604464

Converging on a Semantic Interoperability Framework for the European Data Space for Science, Research and Innovation (EOSC)

Author(s): David, Romain; Baumann, Kurt; Le Franc, Yann; Magagna, Barbara; Vogt, Lars; Widmann, Heinrich; Jouneau, Thomas; Koivula, Hanna; Madon, Bénédicte; Åkerström, Wolmar Nyberg; Ojsteršek, Milan; Scharnhorst, Andrea; Schubert, Chris; Shi, Zhengdong; Tanca, Letizia; Vancauwenbergh, Sadia
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8042997

Data sharing in the Covid-19 era: challenges and opportunities for Italy. Second edition

Author(s): Pesole, Graziano
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4282675

Open Source Secure Data Infrastructure and Processes for Life Sciences (OSSDIP4LIFE)

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Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8091507

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

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Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4315061

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Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4281097

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Author(s): Maddalena Fratelli
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.4524007

The WorkflowHub - a registry for workflows. The Bioschemas workflow profile.

Author(s): Carole Goble
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4012124

Rethinking data sharing in phytolith research: from FAIR phytoliths to key insights for archaeology.

Author(s): Celine Kerfant; Emma Karoune; Carla Lancelotti; Javier Ruiz-Pérez; Juan José García-Granero; Marco Madella
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7152322

QSM4SENIOR: Quantitative susceptibility mapping in the aging of the healthy brain

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Publisher: Zenodo
DOI: 10.5281/zenodo.7303614

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

Author(s): Wittner, Rudolf; Holub, Petr; Geiger, Jörg; Müller, Heimo; Goble, Carole; Soiland-Reyes, Stian; Fairweather, Elliot; Pireddu, Luca; Frexia, Francesca; Mascia, Cecilia; Zanetti, Gianluigi; Nakae, Hiroki; Strambio, Caterina; Moore, Josh; Grunwald, David; Swedlow, Jason
Published in: 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.5074819

ICOPS Workshop Series - Standard Vocabularies and Ontologies

Author(s): Kerfant, Céline; Dunseth, Zachary C.; Ruiz-Pérez, Javier; Harmse, Henriette; Karoune, Emma; Lancelotti, Carla; Bates, Jennifer; Dabengwa, Abraham; García-Granero, Juan José; Ge, Yong; Madella, Marco; Musaubach, Maria Gabriela; Wong, Frances
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.7998409

Reproducibility; Research Objects (RO-Crate) and Common Workflow Language (CWL)

Author(s): Soiland-Reyes, Stian
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5554684

FAIR assessment to FAIR implementation for reproducibility and replicability in phytolith research

Author(s): Karoune, Emma; García-Granero, Juan José; Kerfant, Celine; Lancelotti, Carla; Madella, Marco; Ruiz-Pérez, Javier
Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8308402

Community Building to move forward with FAIR

Author(s): Karoune, Emma; Lancelotti, Carla; Ruiz-Pérez, Javier; García-Granero, Juan José; Madella, Marco; Kerfant, Celine
Published in: 2021
Publisher: Zenodo
DOI: 10.5281/zenodo.5770743

Microbial resources in the European Open Science Cloud: MIRRI contribution to the EOSC-Life project

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Published in: 2023
Publisher: Zenodo
DOI: 10.5281/zenodo.8052706

Automatic, Efficient and Scalable Provenance Registration for FAIR HPC workflows

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Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.7701868

Increasing the FAIRness of Phytolith Data

Author(s): Kerfant, Celine; Karoune, Emma; Lancelotti, Carla; Ruiz-Pérez, Javier; García-Granero, Juan José; Madella, Marco
Published in: 2022
Publisher: Zenodo
DOI: 10.5281/zenodo.6379803

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

Multilingual Data Challenges in Professionalizing Data Stewardship worldwide

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