Project Deliverables & Publications

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

• Sansone, S.; McQuilton, P.; Rocca-Serra, P. et al. (2019). FAIRsharing as a community approach to standards, repositories and policies. Nature Biotechnology 37, 358. https://doi.org/10.1038/s41587-019-0080-8
• Föll, M.; Moritz, L.; Wollmann, T. et al. (2019). Accessible and reproducible mass spectrometry imaging data analysis in Galaxy.  GigaScience 8, 1. https://doi.org/10.1093/gigascience/giz143.
• Wilkinson, M.; Dumontier, M.; Sansone, S. et al. (2019). Evaluating FAIR maturity through a scalable, automated, community-governed framework. Scientific Data 6, 174. https://doi.org/10.1038/s41597-019-0184-5
• Bray, S.; Lucas, X.; Kumar, A. et al. (2020). The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform. Journal of Cheminformatics 12, 40. https://doi.org/10.1186/s13321-020-00442-7. The ChemicalToolbox is used within EOSC-Life’s Demonstrator 1 (Galaxy team).
• Vilas, J.; Tagare, H.; Vargas, J. et al. (2020). Measuring local-directional resolution and local anisotropy in cryo-EM maps. Nature Communications 11, 55.  https://doi.org/10.1038/s41467-019-13742-w
• Rocca-Serra, P.; Sansone, S. (2020). Experiment design driven FAIRification of omics data matrices, an exemplar. Scientific Data 6, 271. https://doi.org/10.1038/s41597-019-0286-0
• Abudukelimu, A.; Barberis, M.; Redegeld, F. et al. (2020). Complex stability and an irrevertible transition reverted by peptide and fibroblasts in a dynamic model of innate immunity. Frontiers in Immunology 10. https://doi.org/10.3389/fimmu.2019.03091
• Goble, C.; Cohen-Boulakia, S.; Soiland-Reyes, S. et al. (2020). FAIR computational workflows. Data Intelligence, 2(1-2), 108.  https://doi.org/10.1162/dint_a_00033
• David, R.; Mabile, L.; Specht, A. et al. (2020). FAIRness literacy: The Achilles’ heel of applying FAIR principles. Data Science Journal, 19(32), 1-11. http://doi.org/10.5334/dsj-2020-032
• Střelák, D.; Filipovič, J.; Jiménez-Moreno, A. et al. (2020). FlexAlign: An accurate and fast algorithm for movie alignment in cryo-electron microscopy. Electronics, 9 (6), 1040.  https://doi.org/10.3390/electronics9061040
• Melero, R.; Sorzano, C.; Foster, B. et al. (2020). Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. International Union of Crystallography Journal, 7(6), 1059. https://doi.org/10.1107/S2052252520012725
• Caracciolo, C.; Aubin, S.; Jonquet, C. et al. (2020). 39 Hints to facilitate the use of semantics for data on agriculture and nutrition. Data Science Journal 19(47), 1. http://doi.org/10.5334/dsj-2020-047
• Jacob, D.; David, R.; Aubin, S. et al. (2020). Making experimental data tables in the life sciences more FAIR: a pragmatic approach. GigaScience 9, 1. https://doi.org/10.1093/gigascience/giaa144
• Obst, M.; Exter, K.; Allcock, A. et al. (2020). A marine biodiversity observation network for genetic monitoring of hard-bottom communities (ARMS-MBON). Frontiers in Marine Science, Frontiers Media 7. https://doi.org/10.3389/fmars.2020.572680
• Vilas, J.; Oton, J.; Messaoudi, C. et al. (2020). Measurement of local resolution in electron tomography. Journal of Structural Biology 4, 100016. https://doi.org/10.1016/j.yjsbx.2019.100016
• Sorzano, C.; de Isidro-Gómez, F.; Fernández-Giménez, E. et al. (2020). Improvements on marker-free images alignment for electron tomography. Journal of Structural Biology 4, 100037. https://doi.org/10.1016/j.yjsbx.2020.100037
• Tanoli, Z.; Seemab, U.; Scherer, A. et al. (2020). Exploration of databases and methods supporting drug repurposing: a comprehensive survey. Briefings in Bioinformatics 22(2), 1656. https://doi.org/10.1093/bib/bbaa003
• Tangaro, M.; Mandreoli, P.; Chiara, M. et al. (2021). Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service. BMC Bioinformatics 22, 544. https://doi.org/10.1186/s12859-01-3
• Sanchez-Garcia, R.; Gomez-Blanco, J.; Cuervo, A. et al. (2021). DeepEMhancer: a deep learning solution for cryo-EM volume post-processing. Communications Biology 4, 874. https://doi.org/10.1038/s42003-021-02399-1
• Pickering B.; Biro, T.; Austin, C. et al. (2021). Radical collaboration during a global health emergency: development of the RDA COVID-19 data sharing recommendations and guidelines. Open Research Europe 1, 69. https://doi.org/10.12688/openreseurope.13369.1
• Holzinger, A.; Müller, H. (2021). Toward human–AI interfaces to support explainability and causability in medical AI. Computer 54(10), 78. https://doi.org/10.1109/MC.2021.3092610
• Fernández-Giménez, E.; Martínez, M.; Sánchez-García, R. et al. (2021). Cryo-EM density maps adjustment for subtraction, consensus and sharpening. Journal of Structural Biology 213 (4), 107780. https://doi.org/10.1016/j.jsb.2021.107780
• Laveglia, V.; Giachetti, A.; Cerofolini, L. et al. (2021). Automated determination of nuclear magnetic resonance chemical shift perturbations in ligand screening experiments: The PICASSO web server. Journal of Chemical Information and Modeling 61(12), 5726. https://doi.org/10.1021/acs.jcim.1c00871
• Lamprecht, A.; Palmblad, M.; Ison, J. et al. (2021). Perspectives on automated composition of workflows in the life sciences. F1000Research, 10, 897. https://doi.org/10.12688/f1000research.54159.1
• Strelak, D.; Jiménez-Moreno, A.; José, L. et al. (2021). Advances in Xmipp for cryo–electron microscopy: from Xmipp to Scipion. Molecules 26(20), 6224. https://doi.org/10.3390/molecules26206224
• Machwitz, M.; Pieruschka, R.; Berger, K. et al. (2021). Bridging the gap between remote sensing and plant phenotyping—challenges and opportunities for the next generation of sustainable agriculture. Frontiers in Plant Science, 12, 749374. https://doi.org/10.3389/fpls.2021.749374
• Macias, J.; Sanchez-Garcia, R.; Conesa, P. et al. (2021). 3DBionotes COVID-19 edition. Bioinformatics 37(22), 4258. https://doi.org/10.1093/bioinformatics/btab397
• Song, F.; Ali Khan,A.; Matteoni, R. et al. (9-12 June 2021). INFRAFRONTIER Supports Targeting Cancer with Animal Models. European Association for Cancer Research (EACR) 2021 Virtual Congress. https://publications.cnr.it/doc/456948
• Rizzo, D.; Cerofolini, L.; Pérez-Ràfols, A. et al. (2021). Evaluation of the Higher Order Structure of Biotherapeutics Embedded in Hydrogels for Bioprinting and Drug Release. Analytical Chemistry, 9(32): 11208–11214.  https://doi.org/10.1021/acs.analchem.1c01850
• Hruska, M.; Holub, D. (2022). A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge. International Journal of Mass Spectrometry 471, 116723. https://doi.org/10.1016/j.ijms.2021.116723
• Machicao, J.; Specht, A.; Vellenich, D. et al. (2022). A deep-learning method for the prediction of socio-economic indicators from street-view imagery using a case study from Brazil. Data Science Journal 21(6), 1. https://doi.org/10.5334/dsj-2022-006
• Zullino, S.; Paglialonga, A.; Dastrù, W. et al. (2022). XNAT-PIC: extending XNAT to preclinical imaging centers. Journal of Digital Imaging. https://doi.org/10.1007/s10278-022-00612-z
• Eiteneuer, C.; Velasco, D.; Atemia, J. et al. (2022). GXP: analyze and plot plant omics data in web browsers. Plants 11(6), 745. https://doi.org/10.3390/plants11060745
• Brack, P.; Crowther, P.; Soiland-Reyes, S. et al. (2022). Ten simple rules for making a software tool workflow-ready. PLOS Computational Biology 18(3), e1009823. https://doi.org/10.1371/journal.pcbi.1009823
• Alharbi, E.; Gadiya, Y.; Henderson, D. et al. (2022). Selection of data sets for FAIRification in drug discovery and development: Which, why, and how? Drug Discovery Today 27(8), 2080. https://doi.org/10.1016/j.drudis.2022.05.010
• Crusoe, M.; Abeln, S.; Iosup, A. et al. (2022). Methods included: Standardizing computational reuse and portability with the common workflow language. Communications of the ACM 65(6), 54. https://doi.org/10.1145/3486897
• Ohmann, C.; David, R.; Cano Abadia, M. et al. (2022). Pilot study on the intercalibration of a categorisation system for FAIRer digital objects related to sensitive data in the life sciences. Data Intelligence 4(2), 196. https://doi.org/10.1162/dint_a_00126
• Soiland-Reyes, S.; Sefton, P.; Crosas, M. et al. (2022). Packaging research artefacts with RO-Crate. Data Science, 1, 1. https://doi.org/10.3233/DS-210053
• Soiland-Reyes S.; Bayarri G.; Andrio P. et al. (2022). Making Canonical Workflow Building Blocks Interoperable across Workflow Languages. Data Intelligence, 4(2), 342. https://doi.org/10.1162/dint_a_00135
• Zaliani, A.; Vangeel, L.; Reinshagen, J. et al. (2022). Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort. Scientific Data, 9, 405. https://doi.org/10.1038/s41597-022-01532-x 
• Laveglia, V.; Giachetti, A.; Sala, D. et al. (2022). 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. Journal of Chemical Information and Modeling, 62(12), 2951. https://doi.org/10.1021/acs.jcim.2c00522
• Massimi, M.; Di Pietro, C.; La Sala, G. et al. (2022). Mouse mutants of Gpr37 and Gpr37l1 receptor genes: disease modeling applications. International Journal of Molecular Sciences, 23(8), 4288. https://doi.org/10.3390/ijms23084288
• Birling, M.; Fray, M.; Kasparek, P. et al. (2022). Importing genetically altered animals: ensuring quality. Mammalian Genome, 33, 100. https://doi.org/10.1007/s00335-021-09908-x
• Hruska, M.; Holub, D. (2022). Evaluation of an integrative Bayesian peptide detection approach on a combinatorial peptide library. European Journal of Mass Spectrometry, 27(6), 217.
• Muller, C.; Serrano-Solano, B.; Sun, Y. et al. (2022). The Image Data Explorer: Interactive Exploration of Image-derived Data. PLoS ONE, 17(9): e0273698. https://doi.org/10.1371/journal.pone.0273698
• Boiten, J.-W.; Ohmann, C.; Adeniran, A. et al. (2022). EOSC-LIFE WP4 TOOLBOX: Toolbox for sharing of sensitive data — a concept description. arXiv, July 2022. https://arxiv.org/abs/2207.14296
• Karoune, E. Assessing Open Science Practices in Phytolith Research. (2022). Open Quaternary, 8(1), 3. http://doi.org/10.5334/oq.88
• Wittner, R.; Mascia, C.; Gallo, M. et al. (2022). Lightweight Distributed Provenance Model for Complex Real–world Environments. Scientific Data 9, 503. https://doi.org/10.1038/s41597-022-01537-6
• Laveglia, V.; Giachetti, A.; Sala, D. et al. (2022). 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. Journal of Chemical Information and Modeling, 62 (12), 2951–2960. https://doi.org/10.1021/acs.jcim.2c00522
• Brack, P.; Crowther, P.; Soiland-Reyes, S. et al. (2022). Ten simple rules for making a software tool workflow-ready. PLoS Computational Biology, 18(3), e1009823. https://doi.org/10.1371/journal.pcbi.1009823
• Frexia, F.; Mascia, C.; Wittner, R. et al. (2022). The Common Provenance Model: Capturing Distributed Provenance in Life Sciences Processes. In Challenges of Trustable AI and Added-Value on Health (pp. 415-416). IOS Press.
• Holzinger, A.; Kargl, M.; Kipperer, B. et al. (2022). Personas for Artificial Intelligence (AI) An Open Source Toolbox. IEEE Access, 10, 23732-23747. https://doi.org/10.1109/ACCESS.2022.3154776
• Soiland-Reyes, S.; Sefton, P.; Castro, L. et al. (2022). Creating lightweight FAIR Digital Objects with RO-Crate. Research Ideas and Outcomes, 8, e93937. https://riojournal.com/article/93937/download/pdf/
• Madeira, F.; Pearce, M.; Tivey, A. et al. (2022). Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic acids research, 50(W1), W276-W279. https://doi.org/10.1093/nar/gkac240
• Serrano-Solano, B.; Fouilloux, A.; Eguinoa, I. et al. (2022). Galaxy: A decade of realising CWFR concepts. Data Intelligence, 4(2), 358-371. https://doi.org/10.1162/dint_a_00136
• Janni, M.; Pieruschka, R. (2022). Plant phenotyping for a sustainable future. Journal of Experimental Botany, 73(15), 5085-5088. https://doi.org/10.1093/jxb/erac286
• Hruska, M. (2022). Identification of variant peptides using mass spectrometry. PhD dissertation (Department of Computer Science, Faculty of Science, Palacky University Olomouc). https://theses.cz/id/1glpu2/Thesis.pdf
• Eva, G.; Liese, G.; Stephanie, B. et al. (2022). Position paper on management of personal data in environment and health research in Europe. Environment International, 165, 107334. https://doi.org/10.1016/j.envint.2022.107334
• Müller, H.; Holzinger, A.; Plass, M. et al. (2022). Explainability and causability for artificial intelligence-supported medical image analysis in the context of the European in vitro diagnostic regulation. New Biotechnology, 70, 67-72. https://doi.org/10.1016/j.nbt.2022.05.002
• Soiland-Reyes, S.; Castro, L.; Garijo, D. et al. (2022). Updating linked data practices for FAIR digital object principles. Research Ideas and Outcomes, 8, e94501. https://riojournal.com/article/94501/download/pdf/
• Hardisty, A.; Brack, P.; Goble, C. et al. (2022). The specimen data refinery: a canonical workflow framework and FAIR digital object approach to speeding up digital mobilisation of natural history collections. Data Intelligence, 4(2), 320-341. https://doi.org/10.1162/dint_a_00134
• Weise, M.; Kovacevic, F.; Popper, N. et al. (2022). OSSDIP: Open Source Secure Data Infrastructure and Processes Supporting Data Visiting. Data Science Journal, 21(1). OSSDIP: Open Source Secure Data Infrastructure and Processes Supporting Data Visiting (codata.org)
• Batista, D.: Gonzalez-Beltran, A.: Sansone, S. et al. (2022). Machine actionable metadata models. Scientific Data 9, 592. https://doi.org/10.1038/s41597-022-01707-6
• Matentzoglu, N.; Balhoff, J.; Bello, S. et al. (2022, 25 May). A Simple Standard for Sharing Ontological Mappings (SSSOM). Database, 2022. https://doi.org/10.1093/database/baac035
• Tanoli, Z.; Aldahdooh, J.; Alam, F. et al. (2022). Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments. Briefings in bioinformatics, 23(1), bbab350. https://doi.org/10.1093/bib/bbab350
• Zheng, S.; Wang, W.; Aldahdooh, J. et al. (2022). SynergyFinder plus: toward better interpretation and annotation of drug combination screening datasets. Genomics, Proteomics & Bioinformatics. https://doi.org/10.1016/j.gpb.2022.01.004
• Machicao, J.; Ben Abbes, A.; Meneguzzi, L. et al. (2022). Mitigation strategies to improve reproducibility of poverty estimations from remote sensing images using Deep Learning. Earth and Space Science, 9(8), e2022EA002379. https://doi.org/10.1029/2022EA002379
• Müller, H.; Kargl, M.; Plass, M. et al. (2022). Towards a taxonomy for explainable AI in computational pathology. In: Chen, F., Zhou, J. (eds) Humanity Driven AI. Springer, Cham. https://doi.org/10.1007/978-3-030-72188-6_15
• Del Rio, M.; Lianas, L.; Aspegren, O. et al. (2022). AI support for accelerating histopathological slide examinations of prostate cancer in clinical studies. In: Mazzeo, P.L., Frontoni, E., Sclaroff, S., Distante, C. (eds) Image Analysis and Processing. ICIAP 2022 Workshops. ICIAP 2022. Lecture Notes in Computer Science, vol 13373. Springer, Cham. https://doi.org/10.1007/978-3-031-13321-3_48
• Douglass Jr, E.; Allaway, R.; Szalai, B. et al. (2022). A community challenge for a pancancer drug mechanism of action inference from perturbational profile data. Cell Reports Medicine, 3(1), 100492. https://doi.org/10.1016/j.xcrm.2021.100492
• Rizzo, D.; Cerofolini, L.; Giuntini, S. et al. (2022). Epitope mapping and binding assessment by solid-state NMR provide a way for the development of biologics under the quality by design paradigm. Journal of the American Chemical Society, 144(22), 10006–10016. https://doi.org/10.1021/jacs.2c03232
• Ciani, C.; Pérez-Ràfols, A.; Bonomo, I. et al. (2022). Identification and characterization of an RRM-containing, RNA binding protein in Acinetobacter baumannii. Biomolecules, 12(7), 922. https://doi.org/10.3390/biom12070922
• Sanchez-Garcia, R.; Macias, J.; Sorzano, C. et al. (2022). BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction. Journal of Molecular Biology, 434(11), 167556. https://doi.org/10.1016/j.jmb.2022.167556
• Sorzano, C.; Vilas, J.; Ramirez-Aportela, E. et al. (2022). Image processing tools for the validation of CryoEM maps. Faraday Discussions. https://doi.org/10.1039/D2FD00059H
• Bray, S.; Dudgeon, T.; Skyner, R. et al. (2022). Galaxy workflows for fragment-based virtual screening: a case study on the SARS-CoV-2 main protease. Journal of Cheminformatics, 14(22). https://doi.org/10.1186/s13321-022-00588-6
• Aldahdooh, J.; Vähä-Koskela, M.; Tang, J. et al. (2022). Using BERT to identify drug-target interactions from whole PubMed. BMC bioinformatics, 23(1), 1-13. https://doi.org/10.1186/s12859-022-04768-x
• de la Morena, J.; Conesa, P.; Fonseca, Y. et al. (2022). ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation. Journal of Structural Biology, 107872. https://doi.org/10.1016/j.jsb.2022.107872
• Sorzano, C.; Jiménez-Moreno, A.; Maluenda, D. et al. (2022). On bias, variance, overfitting, gold standard and consensus in single-particle analysis by cryo-electron microscopy. Acta Crystallographica Section D: Structural Biology, 78(4), 410-423. https://doi.org/10.1107/S2059798322001978
• Plass, M.; Kargl, M.; Evans, T. et al. (2023). Human-AI interfaces are a central component of trustworthy AI. In: Mehta, M., Palade, V., Chatterjee, I. (eds) Explainable AI: Foundations, Methodologies and Applications. Intelligent Systems Reference Library, vol 232. Springer, Cham. https://doi.org/10.1007/978-3-031-12807-3_11
• De Geest, P.; Coppens, F.; Soiland-Reyes, S. et al. (2022). Enhancing RDM in Galaxy by integrating RO-Crate. Research Ideas and Outcomes, 8, e95164. https://riojournal.com/article/95164/download/pdf/
• Massai, L.; Grifagni, D.; De Santis, A. et al. (2022). Gold-based metal drugs as inhibitors of coronavirus proteins: The inhibition of SARS-CoV-2 main protease by auranofin and its analogs. Biomolecules, 12, 1675. https://doi.org/10.3390/biom12111675
• Petek, M.; Zagorščak, M.; Blejec, A. et al. (2022). pISA-tree – a data management framework for life science research projects using a standardised directory tree. Scientific Data 9, 685. https://doi.org/10.1038/s41597-022-01805-5
• Burgin, J.; Ahamed, A.; Cummins, C. et al. (2022). The European Nucleotide Archive in 2022. Nucleic Acids Research, gkac1051, https://doi.org/10.1093/nar/gkac1051
• David, R.; Ohmann, C.; Boiten, JW. et al. (2022) An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data. Science Reports 12, 20989. https://doi.org/10.1038/s41598-022-25278-z
• Matentzoglu, N.; Balhoff, J.; Bello, S. et al. (2022). A Simple Standard for Sharing Ontological Mappings (SSSOM). Database 2022. https://doi.org/10.1093/database/baac035 
• iltemann, S.; Rasche, H.; Gladman, S. et al. (2023). Galaxy Training: A Powerful Framework for Teaching! PLOS Computational Biology 19(1): e1010752. https://doi.org/10.1371/journal.pcbi.1010752
• Cerofolini, L.; Ramberg, K.; Padilla, L. et al. (2023).  Solid-state NMR – a complementary technique for protein framework characterization. Chemical Communications 59: 776-779. https://doi.org/10.1039/D2CC05725E
• Pape, C.; Meechan, K.; Moreva, E. et al. (2023). MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data. Nature Methods (10 Feb 2023). https://doi.org/10.1038/s41592-023-01776-4
• Grifagni, D.; Silva, J.; Cantini, F. et al. (2023). Relaxation-based NMR assignment: Spotlights on ligand binding sites in human CISD3. Journal of Inorganic Biochemistry 239: 112089. https://doi.org/10.1016/j.jinorgbio.2022.112089
• Richardson, L.; Allen, B.; Baldi, G. et al. (2023). MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research 51(D1): D753-D759. https://doi.org/10.1093/nar/gkac1080
• Bazayeva, M.; Giachetti, A.; Pagliai, M. et al. (2023). A Comparison of Bonded and Nonbonded Zinc(II) Force Fields with NMR Data. International Journal of Molecular Sciences 24: 5440. https://doi.org/10.3390/ijms24065440
• Hiltemann, S.; Rasche, H.; Gladman, S. et al. (2023). Galaxy Training: A powerful framework for teaching! PLoS Comput Biol 19(1): e1010752. https://doi.org/10.1371/journal.pcbi.1010752
• Plass, M.; Kargl, M.; Kiehl, T.-R. et al. (12 April 2023). Explainability and causability in digital pathology. J Pathol Clin Res. https://doi.org/10.1002/cjp2.322
• Wittner, R.; Holub, P.; Mascia, C. et al. (2023). Towards a common standard for data and specimen provenance in life sciences. Learning Health Systems: e10365. https://doi.org/10.1002/lrh2.10365
• Chiara, M.; Horner, D.; Ferrandi, E. et al. (2023) HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2. Commun Biol 6, 443. https://doi.org/10.1038/s42003-023-04784-4
• Rocca-Serra, P.; Gu, W.; Ioannidis, V. et al. (2023) The FAIR Cookbook – the essential resource for and by FAIR doers. Sci Data 10, 292. https://doi.org/10.1038/s41597-023-02166-3
• Santi, I.; Beluche, O.; Beraud, M. et al. (2023) European marine omics biodiversity observation network: a strategic outline for the implementation of omics approaches in ocean observation.  Frontiers in Marine Science (May 18, 2023). https://doi.org/10.3389/fmars.2023.1118120
• Kellmann, A. and others, on behalf of the Lifelines Corona Research Initiative. (2023) Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes. Database, 2023, 2023, baad019. https://doi.org/10.1093/database/baad019
• Holub, P.; Müller, H.; Bíl, T. et al. (2023) Privacy risks of whole-slide image sharing in digital pathology. Nat Commun 14, 2577. https://doi.org/10.1038/s41467-023-37991-y
• Agirre, J.; Atanasova, M.; Bagdonas, H. et al. (2023) The CCP4 suite: integrative software for macromolecular crystallography. Structural Biology, 79, 449. https://doi.org/10.1107/S2059798323003595
• David, R.; Burel, J.-M.; Heriche, J.-K. et al. (2023). Sustainability of FAIR Life Science Resources and Projects: Lessons Learned from EOSC-Life Research Infrastructures. Sustainability Sciences (1.0, Preprint) https://doi.org/10.5281/zenodo.8059831
• David, R.; Baumann, K.; Le Franc, Y. et al. (2023). Converging on a Semantic Interoperability Framework for the European Data Space for Science, Research and Innovation (EOSC) (Preprint 1.0.3). 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR) (Onto4FAIR), Sherbrooke, Québec (Canada). Zenodo. https://doi.org/10.5281/zenodo.8102786
• Horák, J.; Furmanová, K.; Kozlíková, B. et al. (2023). xOpat: eXplainable Open Pathology Analysis Tool. Computer Graphics Forum, 42(3), 63. https://doi.org/10.1111/cgf.14812
• Kemmer, I.; Keppler, A.; Serrano-Solano, B. et al. (2023). Building a FAIR image data ecosystem for microscopy communities. Histochem Cell Biol. https://doi.org/10.1007/s00418-023-02203-7
• Hiltemann, S.; Rasche, H.; Gladman, S. et al. (2023). Galaxy Training: A powerful framework for teaching! PLoS Comput Biol 19(1): e1010752. https://doi.org/10.1371/journal.pcbi.1010752
• Kerfant, C.; Ruiz-Pérez, J.; García-Granero, J.J. et al. (2023). A dataset for assessing phytolith data for implementation of the FAIR data principles. Sci Data 10, 479. https://doi.org/10.1038/s41597-023-02296-8
• De Quadros, P.; Gale, N.; and Cerqueira, V. (Eds.). (2023). Management of agroecosystems for enhancement of soil microbial communities and soil natural fertility. Frontiers Media SA.
• Grifagni, D.; Silva, J.; Cantini, F. et al. (2023). Relaxation-Based NMR Assignment: Spotlights on Ligand Binding Sites in Paramagnetic Proteins. J Inorg Biochem 239: 112089. https://doi.org/10.1016/j.jinorgbio.2022.112089
• Silva, J.; Grifagni, D.; Cantini, F. et al. (2023) ¹H, ¹³C and ¹⁵N assignment of the human mitochondrial paramagnetic iron–sulfur protein CISD3. Biomol NMR Assign 17, 17–22. https://doi.org/10.1007/s12104-022-10113-3
• Xu, F., Juty, N., Goble, C. et al. (2023). Features of a FAIR vocabulary. J Biomed Semant 14, 6. https://doi.org/10.1186/s13326-023-00286-8

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

• Bernillon, S.; Cabasson, C.; Cassan, C. et al. (2019) MetaboHUB-Bordeaux. Journées Scientifiques INRA-BAP, Hyères, France. 10.15454/1.5572412770331912E12.
• Zagidullin, B.; Aldahdooh, J.; Zheng, S. et al. (2019) DrugComb – an integrative cancer drug combination data portal. https://doi.org/10.1101/560227
• Jacob, D.; David, R.; Aubin, S. et al. (2020) Towards FAIRification of experimental data tables in life sciences: a pragmatic approach. 10.15454/1.5572412770331912E12
• Fairweather, E.; Wittner, R.; Chapman, M. et al. (June 2020) International Provenance & Annotation Workshop (IPAW). Non-repudiable provenance for clinical decision support systems.  http://arxiv.org/abs/2006.11233
• Bray, S.; Senapathi, T.; Barnett, C. et al. (2020) Intuitive, reproducible high-throughput molecular dynamics in Galaxy: a tutorial. https://doi.org/10.1101/2020.05.08.084780
• Ramirez-Aportela, E.; Maluenda, D.; Fonseca, Y. et al. (2020) FSC-Q: A CryoEM map-to-atomic model quality validation based on the local Fourier Shell Correlation.   https://doi.org/10.1101/2020.05.12.069831
• Sorzano, C.; Crisman, E.; Carazo, J. et al. (2020) Multitarget virtual screening for drug repurposing in COVID19. https://doi.org/10.26434/chemrxiv.12652997.v2
• Goble, C. (2020) The WorkflowHub – a registry for workflows. The Bioschemas workflow profile.  https://doi.org/10.5281/zenodo.4012124
• Canham, S. (August 2021) ECRIN metadata schema for clinical research data objects version 6.0. https://doi.org/10.5281/zenodo.1312538
• Soiland-Reyes, S.; Eguinoa, I. (2021) Packaging workflows with RO-Crate.  https://doi.org/10.5281/zenodo.4011999.
• Zullino, S.; Paglialonga, A.; Dastrù, W. et al. (2021) XNAT-PIC: extending XNAT to preclinical imaging centers. https://arxiv.org/abs/2103.02044
• Rauber, A.; Weise, M.; Landman, M. et al. (2021) Open source secure data infrastructure and processes for life sciences (OSSDIP4LIFE). https://doi.org/10.5281/zenodo.5534008
• Goble, C.; Soiland-Reyes, S.; Bacall, F. et al. (2021). Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory. https://doi.org/10.5281/zenodo.4605654
• Lipok, M.; Obstaczyk, P.; Grelich-Mucha, M. et al. (24 June 2021). Understanding the internal structure of amyloid superstructures with polarization analysis of two-photon excited fluorescence (poster). ELMI 2021. https://www.elmi2021.org/abstract/understanding-the-internal-structure-of-amyloid-superstructures-with-polarization-analysis-of-two-photon-excited-fluorescence.html 
• Kerfant, C.; Karoune, E.; Lancelotti, C. et al. (2022) Increasing the FAIRness of phytolith data. https://doi.org/10.5281/zenodo.6379803
• Abbes, A.; Machicao, J.; Meneguzzi, L. et al. (2022) Checklist strategies to improve the reproducibility of deep learning experiments with an illustration.  https://doi.org/10.5281/zenodo.6587702
• Machicao, J.; Abbes, A.; Meneguzzi, L. et al. (2022) Deep learning experiments: common challenges and recommendations for improvement. https://doi.org/10.5281/zenodo.6587694
• Epinoux, C.; Castrec, J.; David, R. et al. (2022) Good practices and challenges for sharing multidisciplinary scientific data: How the QUAMPO project fits into the FAIR and open science movement? https://doi.org/10.5281/zenodo.6779714
• Karoune, E.; Barboni, D.; Bates, J. et al. (2022) Open phytolith publishing guidelines (Version v1). https://doi.org/10.5281/zenodo.6803489
• Coppens, F. (2022) usegalaxy.be. https://doi.org/10.5281/zenodo.6607021
• Karoune, E., Plomp, E. (2022) Removing barriers to reproducible research in archaeology (Version v2). https://doi.org/10.5281/zenodo.6618672
• Coppens, F. (2022) Building an interoperable genomic data infrastructure.  https://doi.org/10.5281/zenodo.6604464
• Portier, M.; Decruw, C.; Exter, K. et al. (2022) Contemporary data management for biodiversity observation networks leading to linked open data publishing through distributed techniques applying RO-Crate and GitHub actions. Biodiversity Information Science and Standards 6: e94630. https://doi.org/10.3897/biss.6.94630
• Niehues, A.; de Visser, C.; Hagenbeek, F. et al. (2022) A multi-omics data analysis workflow packaged as a FAIR digital object. Research Ideas and Outcomes 8: e94042. https://doi.org/10.3897/rio.8.e94042
• Rocca-Serra, P.; Gu, W.; Ioannidis, V. et al. (2022) The FAIR Cookbook – the essential resource for and by FAIR doers (Preprint, Version 1.0). https://doi.org/10.5281/zenodo.7156792
• Musaubach, M. (September 20, 2022) Ubicación y traducción. Evento de lanzamiento de la Comunidad de Fitolitos Abiertos.  https://doi.org/10.5281/zenodo.7098061
• Grannel, R.; Dauga, D.; Lister, A. et al. (2022) Semi-automatic mapping of external scientific databases into the FAIRsharing platform (Presentation, Version 1.0, RSECon2022). https://doi.org/10.5281/zenodo.7064637
• Karoune, E.; Plomp, E. (2022) Removing Barriers to Reproducible Research in Archaeology (Preprint, Version v3). https://doi.org/10.5281/zenodo.7239193
• Holub, P.; Müller, H.; Bil, T. et al. (2022) Privacy Risks of Whole-Slide Image Sharing in Digital Pathology (preprint). medRxiv. https://doi.org/10.1101/2022.04.06.22273523
• Wang, Y.; Aldahdooh, J.; Yang, H. et al. (2022) DrugRepo: A novel approach to repurpose a huge collection of compounds based on chemical and genomic features. Scientific Reports, 12 (1) https://doi.org/10.1101/2022.04.21.488995
• Cerofolini, L.; Rizzo, D.; Giuntini, S. et al. (2022). Solid-state NMR spectra of the complex of PD-L1 with the anti-PD-L1 fusion protein and of the mixture of PD-L1 with a non-binding mAb [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6363169
• Romano, P; Rosato, A.; EOSC-Life project Consortium. (June 27-29, 2022) Recent achievements of the EOSC-Life project. 18th Annual Meeting of the Italian Bioinformatics Society BITS 2022, Verona, Italy.
• Karoune, E.; García-Granero, J.; Lancelotti, C. et al.  (September 27, 2022) Open Phytoliths Community Launch Event Presentations. https://doi.org/10.5281/zenodo.7090455
• Goble, C.; Soiland-Reyes, S. (October 5, 2022). RO-Crate: packaging metadata love notes into FAIR Digital Objects (Presentation, HMC/IAPS Conference 2022).  https://doi.org/10.5281/zenodo.7147703
• Kerfant, C.; Karoune, E.; Lancelotti, C. et al. (October 6, 2022). Rethinking data sharing in phytolith research: from FAIR phytoliths to key insights for archaeology (Presentation, EEA Annual Meeting 2022). https://doi.org/10.5281/zenodo.7152322
• Karoune, E. García-Granero, J., Lancelotti, C. et al. (September 27, 2022) Open Phytoliths Community Launch Event Presentations. https://doi.org/10.5281/zenodo.7090455
• Guevara, M.; Cam, D.; Badagbon, J. et al. (October 16, 2022) QSM4SENIOR: Quantitative susceptibility mapping in the aging of the healthy brain. (QMR a joint workshop on MR phase, magnetic susceptibility and electrical properties mapping. Lucca, Italy.) https://doi.org/10.5281/zenodo.7303615
• Clark-Casey, J., Soiland-Reyes, S. (November 16, 2022) Making EOSC Research Objects FAIR with RO-Crate: A common metadata overlay for EOSC repositories. (Talk presented at EOSC Symposium 2022, Prague, CZ.) https://doi.org/10.5281/zenodo.7323480
• Wang, W.; Bao, J.; Zheng, S. et al. (November 8, 2022) A gene essentiality signature for studying the mechanism of action of drugs. (bioRxiv preprint). https://doi.org/10.1101/2022.11.07.514541 
• David, R.; Epinoux, C.; Barbarin, M. et al. (2022). How the WIBE initiative follows the FAIR principles and open science requirements. (Talk #6, provided at the EOSC Symposium 2022, 15 November 2022). (PDF) How the WIBE initiative follows the FAIR principles and open science requirements (Talk #6) (researchgate.net)
• Holub, P.; Müller, H.; Bíl, T. et al. (January 12, 2023). Privacy Risks of Whole-Slide Image Sharing in Digital Pathology. (medRxiv preprint). https://doi.org/10.1101/2022.04.06.22273523
• David, R.; Richard, A.; Connellan, C. et al. (2023). Umbrella Data Management Plans to Integrate FAIR Data: Lessons from the ISIDORe and BY-COVID Consortia for Pandemic Preparedness. (Data Science Journal preprint). https://doi.org/10.5281/zenodo.7520086
• Kemmer, I.; Keppler, A.; Serrano-Solano, B. et al. (2023). Building a FAIR image data ecosystem for microscopy communities. Zenodo. https://doi.org/10.5281/zenodo.7788899
• Karoune, E.; Lancelotti, C.; Bates, J. et al. (2023, March 24). Using Repositories Workshop. Zenodo. https://doi.org/10.5281/zenodo.7717229.
• Romano, P. & Rosato, A. EOSC-Life project Consortium. Recent achievements of the EOSC-Life project. 18th Annual Meeting of the Italian Bioinformatics Society BITS 2022, June 27-29, 2022, Verona, Italy.
• Rahman, N.; O’Cathail, C.; Zyoud, A. et al. (2023) Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses. bioRxiv 2023.04.19.537514. https://doi.org/10.1101/2023.04.19.537514
• Schmidt-Tremmel, F.; Blomberg, N.; Crockett, S. (2023, version 1, poster) Populating EOSC-Life. F1000Research 2023, 12(ELIXIR):553. https://doi.org/10.7490/f1000research.1119420.1
• Julia, J. (2023). Scanpy Parameter Iterator – Galaxy Training Material [Data set]. Zenodo. https://doi.org/10.5281/zenodo.8016679
• Romano, P.; Aznar, R.; López Coronado, J. et al. (2023). Microbial resources in the European Open Science Cloud: MIRRI contribution to the EOSC-Life project (Poster, Version 0). Zenodo. https://doi.org/10.5281/zenodo.8052706
• Karoune, E.; Lancelotti, C.; Kerfant, C. et al. (2023, June 16). Open Research Skills Workshops – Open access publishing video. Zenodo. https://doi.org/10.5281/zenodo.8047749
• Kerfant, C.; Dunseth, Z.; Ruiz-Pérez, J. et al. (2023, June 2). ICOPS Workshop Series – Standard Vocabularies and Ontologies. Zenodo. https://doi.org/10.5281/zenodo.8047482
• van Gelder, C. (2023, June 13). FAIR Data Stewardship Training & Capacity Building. Presentation at the EOSC-Life/Health-RI workshop Bridging the gap between researchers and the Health & Life Sciences research infrastructures, 13-14 June 2023, Utrecht, The Netherlands (hybrid meeting). Zenodo. https://doi.org/10.5281/zenodo.8031710
• Soiland-Reyes, S.; Leo, S.; Castro, L. et al. (2023). Sharing data as machine-actionable objects using RO-Crate, Bioschemas and Signposting (poster). ELIXIR All Hands 2023, Dublin, Ireland. Zenodo. https://doi.org/10.5281/zenodo.8004796
• Leo, S.; Rodríguez-Navas, L.; Fernández, J. et al. (2023). Making workflow provenance FAIR across workflow systems with Workflow Run RO-Crate (poster). Elixir All Hands 2023, Dublin, Ireland. Zenodo. https://doi.org/10.5281/zenodo.8004793
• Wittner, R.; Gallo, M.; Leo, S. et al. (2023). Linking provenance and its metadata for an AI-based computation using CPM and RO-Crate [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7924183
• Horák, J. (Spring 2023). Whole Slide Image Viewer for Pathological Data (Master’s Thesis). Department of Visual Computing, Masaryk University, Brno, Czech Republic. https://is.muni.cz/th/aa9ty/xOpat_-_eXplainable_Open_Pathology_Analysis_Tool.pdf
• Soiland-Reyes, S.; Goble, C.; Groth, P. (2023). Evaluating FAIR Digital Object and Linked Data as distributed object systems. arXiv preprint https://doi.org/10.48550/arXiv.2306.07436
• Guevara, M.; Cam, D.; Badagbon, J. et al. (27 March 2023). Common Workflow Language & European Open Science Cloud pour l’implémentation de l’imagerie Quantitative de Susceptibilité Magnétique (QSM) du cerveau (poster). 6e congrès scientifique de la Société Française de Résonance Magnétique en Biologie et Médecine in Paris, France. Zenodo. https://doi.org/10.5281/zenodo.7871306
• Weise, M. (20 April 2023). Repository and Compute Environment for Sensitive Data [Conference Presentation]. BioImaging and the European Open Science Cloud, Heidelberg, Germany. https://doi.org/10.34726/3946
• Jakiela, J.; Rasche, H.; Videm, P. et al. (17 May 2023). Inferring Trajectories Using Monocle3 (R). Galaxy Training. https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scrna-case_monocle3-rstudio/tutorial.html
• Guevara, M.; Cam, D.; Badagbon, J. et al. (19 May 2023). Automated brain QSM computation pipeline deployed in the European Open Science Cloud (poster). International Society for Magnetic Resonance in Medicine (ISMRM) 2023. https://doi.org/10.5281/zenodo.8065800
• David, R.; Madon, B.; Torralba, A. (12 June 2023). Introduction to Semantic Interoperability Challenges for RIs (Webinar). Zenodo. https://doi.org/10.5281/zenodo.8077518
• Weise, M.; Grantner, T.; Karnbach, G. et al. (28 June 2023). Open Source Secure Data Infrastructure and Processes for Life Sciences (OSSDIP4LIFE) (Conference Presentation). Zenodo. https://doi.org/10.5281/zenodo.8091507
• Abadía, M.; Cirillo, D.; Cortés, A. (2023, July 25). Train-the-Trainer – Integration of the sex and gender dimension in life sciences research (slides). Zenodo. https://doi.org/10.5281/zenodo.8183682
• Sandström, M.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing content: standards overview (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186982
• Pelletier, G.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing content: databases overview (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186961
• Thorpe, D.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: researchers (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186952
• Burrows, K.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: journal publishers (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186640
• Wulff, E.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: funders (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186623
• Partridge, A.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: librarians, trainers, data stewards (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186609
• Mitrea, G.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: developers and curators (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186594
• Anderson, L.; Lister, A.; Sansone, S. (2023, July 26). FAIRsharing for you: societies and alliances (lesson). Zenodo. https://doi.org/10.5281/zenodo.8186504
• Lister, A. and Sansone, S. (2023, July 28). FAIRsharing in a nutshell (factsheet). Zenodo. https://doi.org/10.5281/zenodo.8191958
• David, R.; Baumann, K.; Le Franc, Y. et al. (2023, August 2). Converging on a Semantic Interoperability Framework for the European Data Space for Science, Research and Innovation (EOSC) (oral presentation at the 2nd Workshop on Ontologies for FAIR and FAIR Ontologies (Onto4FAIR), July 17-19, 2023 Sherbrooke, Québec). Zenodo. https://doi.org/10.5281/zenodo.8209833
• David, R.; Rybina, A.; Burel, J.-M. et al. (2023). “Be Sustainable Recommendations” for FAIR Resources in Life Sciences research: EOSC-Life’s Lessons (preprint). Sustainability Sciences (6.1). Zenodo. https://doi.org/10.5281/zenodo.8247376
• Karoune, E.; Lancelotti, C.; Bates, J. et al. (2023, September 6). Progress towards open science in phytolith research: International Committee on Open Phytolith Science (ICOPS). Presentation at the 13th International Meeting on Phytolith Research in Israel. Zenodo. https://doi.org/10.5281/zenodo.8287353

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

• Deliverable D1.1 — EOSC Cloud feasibility assessment for Demonstrators (Aug 2020)
• Deliverable D1.3: FAIR services deployment for open calls (February 2022)
• Deliverable D2.1 — Cloud implementation of exemplary workflows (Aug 2020)
• Deliverable D2.2: EOSC-Life A common environment that can run cross-RIs workflows. (October 2022)
• Deliverable D2.3: EOSC-Life Implementation of a mechanism for publishing and sharing workflows across instances of the environment. (May 2023)
• Deliverable D3.1 — Publication of generic guidelines for the organization of topic-specific Open Calls (Sep 2020)
• Deliverable D3.2 — Report on the work of the initial demonstrators (May 2021)
• Deliverable D3.3.: EOSC-Life Report on the work of the Open Call Projects. (August 2023)
• Deliverable D4.1: Requirements for Hosting/Distributing and Access Control for Sensitive Data (August 2022)
• Deliverable D4.2 — Report on requirements for regulatory compliance of sensitive health data and biological and medical research data (May 2020)
• 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)
• Deliverable D4.4: Report on data standards for observational and interventional studies, and interoperability between healthcare and research data (December 2021)
• Deliverable D4.5: EOSC-Life Public database inventorying the national health databases and registries and describing their access procedures for reuse for research purposes. (October 2022)
• Deliverable D5.1 – Access and User Management System for Life Science – The Blueprint (Sep 2019)
• Deliverable D5.2 — Access and User Management System for Life Science – the implementation and usage report (Feb 2021)
• Deliverable D5.3 — Access and User Management System for Life Science – the blueprint: 1st update (March 2021)
• Deliverable D5.4 — EOSC-Life Access and User Management System for Life Science – the blueprint update (June 2022)
• Deliverable D5.5.: EOSC-Life Access and User Management System for Life Science – the implementation and usage report. (July 2023)
• Deliverable D6.1 – FAIR Requirements Document  (March 2020)
• Deliverable D6.2 — Common Provenance Model (April 2021)
• Deliverable D6.3: FAIRsharing Webpage (August 2022)
• Deliverable D6.4: EOSC-Life FAIR assistance. (August 2023)
• Deliverable D6.5: EOSC-Life Report on identification and application of registries for FAIR data infrastructures. (August 2023)
• Deliverable D6.6: EOSC-Life Common provenance model for processing biological material, data generation and computational workflows. (August 2023)
• Deliverable D7.1 — Initial EOSC-LS Cloud Observatory Report (Aug 2020)
• Deliverable D7.2 — EOSC-Life final EOSC-LS cloud observatory report (June 2022)
• Deliverable D8.1: EOSC-Life Methodology framework to enhance reproducibility within EOSC-Life – revised version. (September 2022)
• Deliverable D8.2: EOSC-Life Common Framework for Quality, Data and Service Management. (August 2023)
• Deliverable D8.3: EOSC-Life Summary report Stakeholder Forum. (August 2023)
• Deliverable D8.4: EOSC-Life Report on reproducibility. (August 2023)
• Deliverable D9.1 — Final report of analysis of the training needs of different EOSC-Life users (Feb 2020)
• Deliverable D9.2 — Review of EOSC-Life training activities, their impact and potential adaptations (Feb 2021)
• Deliverable D9.3: EOSC-Life Final report on EOSC-Life training activities and their impact. (June 2023)
• Deliverable D10.1 — Strategic Marketing and Stakeholder Mapping Report (Feb 2021)
• Deliverable D10.2: EOSC-Life Review of Effectiveness and Impact of Outreach and Stakeholder Engagement. (August 2023)
• Deliverable D11.1 — Data Management Plan (Aug 2020)
• Deliverable D11.2 — Life Science in EOSC: Summary of EOSC-Life impact and key results (August 2021)
• Deliverable D11.3: EOSC-Life Summary of EOSC-Life Main Achievements and Impacts with Sustainability and Exploitation Plans. (August 2023)
• Deliverable D12.1 (Confidential) (Aug 2020)
• Deliverable D13.1 — Enhanced COVID-19 Portal and data mobilisation reporting (Nov 2021)
• Deliverable D13.2: Data Mobilisation Summary (September 2022)
• Deliverable D14.1 — Strategic plan for the development of a COVID-19 repository including specification of technical requirements, policies and procedures (Oct 2020)
• Deliverable D14.2 — Report about technical implementation and validation of the COVID-19 portal (May 2022)
• Deliverable D14.3: EOSC-Life Report about use and user satisfaction of the COVID-19 repository, including a maintenance and sustainability plan. (April 2023)
• Deliverable D14.4: EOSC-Life Project plan for optional services and future cooperation with IDDO. (August 2023)

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

Newsletter 9 – 19 April 2021

Newsletter 10 – 17 June 2021

Newsletter 11 – 21 October 2021

Newsletter 12 – 16 December 2021

Newsletter 13 – 2 March 2022

Newsletter 14 – 2 May 2022

Newsletter 15 – 30 June 2022

Newsletter 16 – 22 September 2022

Newsletter 17 – 17 November 2022

Newsletter 18 – 26 January 2023

Newsletter 19 – 23 March 2023

Newsletter 20 – 25 May 2023

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• Karoune, E.; Lancelotti, C.; Ruiz-Pérez, J. et al. (10 April 2023). Communicating phytolith data transparently and reproducibility using the FAIR data principles. Talk given at the Integrated Microscopy Approaches in Archaeobotany Workshop. Zenodo. https://doi.org/10.5281/zenodo.7813204
• Karoune, E.; Lancelotti, C.; Bates, J. et al. (24 March 2023). Using Repositories Workshop. Part of a series of a series of workshop about Open Research Skills. Zenodo. https://doi.org/10.5281/zenodo.7717229
• Sirvent, R.; Conejero, J.; Lordan, F. et al. (14 November 2022). Automatic, Efficient and Scalable Provenance Registration for FAIR HPC workflows. Presentation given at the 17th Workshop on Workflows in Support of Large-Scale Science (WORKS 2022), Dallas, TX, USA. Zenodo. https://doi.org/10.5281/zenodo.7701868
• Karoune, E.; Bates, J.; Lancelotti, C. et al. (3 March 2023). Open Access Publishing Workshop. Part of a series of a series of workshop about Open Research Skills. Zenodo. https://doi.org/10.5281/zenodo.7669467
• David, R.; Specht, A.; O’Brien, M. et al. (20–23 June 2022). Multilingual Data Challenges in Professionalizing Data Stewardship worldwide (V1.1). Poster presented at the RDA 19th Plenary Meeting, Part Of International Data Week, Seoul, South Korea. Zenodo. https://doi.org/10.5281/zenodo.6588167
• Woolland, O.; Brack, P.; Soiland-Reyes, S. et al. (2022). Incrementally building FAIR Digital Objects with Specimen Data Refinery workflows. 1st International Conference on FAIR Digital Objects (FDO2022), Leiden, The Netherlands. Zenodo. https://zenodo.org/record/7233688
• Soiland-Reyes, S.; Sefton, P.; Jael Castro, L. et al. (2022). Creating lightweight FAIR Digital Objects with RO-Crate and FAIR Signposting. 1st International Conference on FAIR Digital Objects (FDO2022), Leiden, The Netherlands. Zenodo. https://doi.org/10.5281/zenodo.7245315
• Serrano-Solano, B. (30 June 2022). Galaxy in EOSC-Life. Talk given at the ELIXIR All Hands 2022. F1000Research. https://doi.org/10.7490/f1000research.1119100.1
• Schmidt-Tremmel, F. (2022). EOSC-Life – Building a Digital Space for the Life Sciences. Poster presented at the ELIXIR All Hands 2022. F1000Research. https://doi.org/10.7490/f1000research.1119018.1
• Cano Abadía, M.; Adeniran, A.; Ahern, C. et al. (2022). BBMRI-ERIC ELSI Knowledge Base. Poster presented at the Europe Biobank Week 2021. Zenodo. https://zenodo.org/record/7016638
• David, R.; Burton, N.; Davidson, S. et al. (2021). RDA Sensitive Data IG: Towards a common understanding of sensitive data across regions and disciplines. Poster presented at the RDA 18 Meeting. Zenodo. https://doi.org/10.5281/zenodo.5663084
• David, R.; Ohmann, C.; Boiten, J.-W. et al. (2021). EOSC-Life pilot study on the intercalibration of a categorisation system for FAIRer digital objects related to sensitive data in the life sciences. Poster presented at the RDA 18 Meeting. Zenodo. https://doi.org/10.5281/zenodo.5729437 
• Wittner, R.; Holub, P.; Geiger, J. et al. (2022). Biotechnology – Provenance Information Model for Biological Specimen and Data. Poster presented at the Jason 4th Provenance Week 2020. Zenodo. https://zenodo.org/record/3901011. EOSC-Life version here.
• David, R.; Richard, A.; Stepanyann, D. et al. (2020). Issues and obstacles to the sharing of sensitive data in Europe, who are the stakeholders and what are their responsibilities? (Version 1.0). Zenodo. https://zenodo.org/record/4293611Poster presented at the:
  • CODATA and GO FAIR International FAIR Convergence Symposium (FAIR Convergence Symposium), France.
  • 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)

• Via, A. (21 July 2020). The main European initiatives for sharing data and other research results in support of the scientific community. ELIXIR (Covid-19 data portal), OpenAIRE, RDA. Open Science e COVID-19. Collaborare per contrastare la pandemia. Zenodo. https://doi.org/10.5281/zenodo.3957480
• Via, A. (16 November 2020). 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”.
• Coppens, F. (16 December 2020). Enabling & stimulating submission to the COVID data portal & re-use of the data. 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. Zenodo. https://doi.org/10.5281/zenodo.4326600
• Fratelli, M. (2021, February 9). How in silico methods and data reuse can help reduce the number of animal experiments. Presentation at the conference  “Towards replacement of animals for scientific purposes”. Zenodo. https://doi.org/10.5281/zenodo.4524007
• David, R.; Bouveret, L.; Coché, L. et al. (2021). Data dictionary cookbook for research data and software interoperability at global scale (Version 1.0). Presented at the Research Data Alliance Plenary 17 (RDA P17), Edinburg. Zenodo. http://doi.org/10.5281/zenodo.4683066
• David, R.; Akmon, D.; Burton, N. et al. (2021). RDA Sensitive Data Interest Group: Goals and Roadmap. Zenodo. http://doi.org/10.5281/zenodo.4690571
• Sánchez, I.; Caño, L.; Sorzano, C. (2021). FAIRness in Cryo-Electron Microscopy data analysis. FAIR Metrics and data quality session at the EOSC Symposium 2021 (https://www.eoscsecretariat.eu/eosc-symposium-2021).
• David, R.; Specht, A.; O’Brien, M. et al. (20-23 June 2022). Multilingual Data Challenges in Professionalizing Data Stewardship worldwide (V1.1).  RDA 19th Plenary Meeting, Part Of International Data Week, 20–23 June 2022, Seoul, South Korea. Zenodo.  https://doi.org/10.5281/zenodo.6587896
• Machicao, J.; Abbes, A.; Meneguzzi, L. et al. (2022). Reproducing Deep Learning experiments: common challenges and recommendations for improvement. RDA 19th Plenary Meeting, Part Of International Data Week (RDA Plenary 19th), Seoul, South Korea. Zenodo. https://doi.org/10.5281/zenodo.6587694
• Machicao, J.; Abbes, A.; Meneguzzi, L. et al. (2022). Reproducing Deep Learning experiments: common challenges and recommendations for improvement. RDA 19th Plenary Meeting, Part Of International Data Week (RDA Plenary 19th), Seoul, South Korea. Zenodo. https://doi.org/10.5281/zenodo.6587694
• Abbes, A.; Machicao, J.; Meneguzzi, L. et al. (2022). Checklist Strategies to Improve the Reproducibility of Deep Learning Experiments with an Illustration. RDA 19th Plenary Meeting, Part Of International Data Week (RDA 19), Seoul, South Korea. Zenodo. https://doi.org/10.5281/zenodo.6587702
• Epinoux, C.; Castrec, J.; David, R. et al. (2022). Good practices and challenges for sharing multidisciplinary scientific data: how the QUAMPO project fits into the FAIR and open science movement? RDA 19th Plenary meeting, Seoul, Republic of Korea. Zenodo. https://doi.org/10.5281/zenodo.6779714
• Romano, P.; Rosato, P. (2022). Recent achievements of the EOSC-Life project. Poster presented at the 18th Annual Meeting of the Bioinformatics Italian Society, BITS 2022, Verona, Italy.

In December 2021, EOSC-Life was asked to submit a project brief to the European Commission highlighting milestones toward integration with the European Open Science Cloud and including recommendations for future priorities within the EOSC.

Read the project brief

The EOSC Science Cluster projects sent a joint letter to the EOSC Association and the European Commission in September 2021 arguing for the continuation of the Science Cluster activities in the HEU Work Programme for Research Infrastructures 2023-2024.

View here

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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.

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