Deliverables Open Research Data Pilot (1) DMP - Data Management Plan CINECA is part of the Open Research Data Pilot (ORDP) and the consortium will therefore submit a first version of a Data Management Plan (DMP) as a deliverable within the first 6 months of the project. The DMP will be updated over the course of the project whenever significant changes arise, such as (but not limited to): - new data - changes in consortium policies (e.g. new innovation potential, decision to file for a patent) - changes in consortium composition and external factors (e.g. new consortium members joining or old members leaving). The DMP will be prepared using the template provided by the Commission (http://ec.europa.eu/research/participants/docs/h2020-funding-guide/cross-cutting-issues/open-access-data-management/data-management_en.htm). Documents, reports (11) Training Programme, detailed Training Programme a detailed plan of the training programme for the final two years of the project Training Programme - annual report Training Programme Brief annual report on the training delivered shortterm reach and impact Training programme Brief annual reports on the training delivered shortterm reach and impact for the first three years of the project Report at mo 24 to provide a detailed plan of the training programme for the final two years of the project CINECA Risk Management Registry The CINECA Risk Management Registry.The Project Management team will develop a risk management and contingency plan. Risks in CINECA will be assessed in the areas of data security, ethics, dissemination, innovation, and scientific quality. The contingency plan will ensure that items at risk will be closely monitored and if needed followed-up and controlled. Catalog of Canada, European and African ethical and legal gaps identified A catalog of Canada European and African ethical and legal gaps to identify the legal and ethical gaps and roadblocks impairing future collaborations among the cohorts participating in this consortium We will focus on the legal and ethical requirementsrelated to informed consent secondary use of data and cross border exchanges of data between Europe and third countries We will base our analysis on the potential application of the GDPR to transnational datasamples exchanges on the Canadian domestic laws PIPEDA and H3Africa governance and on the respect on the ethical values stated byinternational policies A report on how the GA4GH researcher ID specifications have been implemented in the ELIXIR AAI A report on how ELIXIR and CanDIG AAI systems will be upgraded to support the GA4GH Library Card concept Semantic and harmonisation best practice A report on Semantic and harmonisation best practice to identify the current coding standards for each cohort and the variables recorded for each of the projects cohort Catalogue on ELSI Issues V1.0 A catalogue of the ethical, legal and social issues for international collaboration of cohorts with a special focus on Europe, Canada and Africa noting the cloud context. The mapping exercise will be achieved by literature as well as legal and policy documents. Report of CINECA kick off meeting A report of CINECA kick off meeting. Report on trust model for partner sites, and between sites and controlled-access researchers A report on trust model for partner sites, and between sites and controlled-access researchers. A machine readable consent ontology mapping of individual cohorts will be used as input to determine the appropriate trust model for partner sites, and between sites and controlled-access researchers. Outreach and dissemination plan A report summarising the outcome of our stakeholder analysis (including training needs analysis), highest priority stakeholder groups and plan for engaging with them throughout the project. This will incorporate a detailed training plan for the first two years of the project and an outline plan for the second two years. Other (4) Text mining processing pipeline for semi structured data A text mining processing pipeline to extract meta data content from semi or unstructured text in documents Access representation ontology developed for project's cohorts Access representation ontology developed for projects cohorts D35 will refine extend and integrate access representations for cohorts based on feedback from WP17 prior work DUO ADAM and user requirements for the cohort access representation Cohort minimal meta data model The common minimal metadata model is intended to function supporting the analytical translational and federation use cases described in WP124 and 5 There are several nascent models in existence in this space though many of these as yet are untested in a HTP production environment of the type to be delivered by CINECA eg EDMI from EOSC and the GA4GH Clinical and Phenotypic Model Therefore we will locate merge and test the models for the use cases coming from the implementation work packages to ensure they are fit for purpose for CINECA Framework and APIs for executing federated genomics analyses Framework and APIs for executing federated genomics analyses We will coordinate with an existing ELIXIR Compute platform project to establish interoperable execution platforms at CSC and EMBLEBI using the Toil framework We will collaborate with the ELIXIR Compute platform environments at CSC and EBI to implement new APIs Demonstrators, pilots, prototypes (3) Query expansion services As part of the Discovery portal T141 we will deliver services for expanding interactive user queries for phenotype and genotype metadata WP3 CanDIG and ELIXIR AAI interoperability demonstration A public demonstration of showing technical integration and interoperability between Europe and Canada AAI systems Discovery service catalog A discovery service catalog by which users will be able to search the datasets by genomic information as well as using the variable related metadata standards developed as part of WP4. The unique contribution of CINECA will be the first unified multidimensional cohort discovery platform that can perform real-time search across a disparate set of cohort infrastructures in Canada, Europe, and Africa. Publications (8) Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory Author(s): Alexander Bernier, Fruzsina Molnár-Gábor, Bartha M Knoppers, Pascal Borry, Priscilla M D G Cesar, Thijs Devriendt, Melanie Goisauf, Madeleine Murtagh, Pilar Nicolás Jiménez, Mikel Recuero, Emmanuelle Rial-Sebbag, Mahsa Shabani, Rebecca C Wilson, Davide Zaccagnini, Lauren Maxwell Published in: European Journal of Human Genetics, 2023, ISSN 1476-5438 Publisher: Nature DOI: 10.1038/s41431-023-01403-y Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service Author(s): Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch Published in: Studies in Health Technology and Informatics, Issue Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Page(s) 839 - 843 Publisher: IOS Press DOI: 10.3233/shti220603 Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature Author(s): Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch Published in: Studies in Health Technology and Informatics, Issue Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Page(s) 876 - 877 Publisher: IOS Press DOI: 10.3233/shti220614 Assessing the use of supplementary materials to improve genomic variant discovery Author(s): Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch Published in: Database, Issue Volume 2023, 2023, ISSN 1758-0463 Publisher: Oxford University Press DOI: 10.1093/database/baad017 Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci Author(s): Nurlan Kerimov, Ralf Tambets, James D. Hayhurst, Ida Rahu, Peep Kolberg, Uku Raudvere, Ivan Kuzmin, Anshika Chowdhary, Andreas Vija, Hans J. Teras, Masahiro Kanai, Jacob Ulirsch, Mina Ryten, John Hardy, Sebastian Guelfi, Daniah Trabzuni, Sarah Kim-Hellmuth, Will Rayner, Hilary Finucane, Hedi Peterson, Abayomi Mosaku, Helen Parkinson, Kaur Alasoo Published in: BioRxiv, 2023 Publisher: Cold Spring Harbor Laboratory DOI: 10.1101/2023.04.06.535816 Training Infrastructure as a Service Author(s): Helena Rasche, Cameron Hyde, John Davis, Simon Gladman, Nate Coraor, Anthony Bretaudeau, Gianmauro Cuccuru, Wendi Bacon, Beatriz Serrano-Solano, Jennifer Hillman-Jackson, Saskia Hiltemann, Miaomiao Zhou, Björn Grüning, Andrew Stubbs Published in: Gigascience, Issue 2022 Dec 28;12:giad048, 2023, ISSN 2047-217X Publisher: Oxford Academy DOI: 10.1093/gigascience/giad048 Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature Author(s): Julien Knafou, Quentin Haas, Nikolay Borissov, Michel Counotte , Nicola Low, Hira Imeri, Aziz Mert Ipekci, Diana Buitrago-Garcia, Leonie Heron, Poorya Amini, Douglas Teodoro Published in: Systematic Reviews, Issue Systematic Reviews 12, Article number: 94 (2023), 2023, ISSN 2046-4053 Publisher: BioMed Central DOI: 10.1186/s13643-023-02247-9 Beacon v2 and Beacon networks: A “lingua franca” for federated data discovery in biomedical genomics, and beyond Author(s): Jordi Rambla, Michael Baudis, Roberto Ariosa, Tim Beck, Lauren A Fromont, Arcadi Navarro, Rahel Paloots, Manuel Rueda, Gary Saunders, Babita Singh, John D Spalding, Juha Törnroos, Claudia Vasallo, Colin D Veal, Anthony J Brookes Published in: Human Mutation, Issue 2022 Jun;43(6), 2022, Page(s) 791-799, ISSN 1098-1004 Publisher: Wiley Online Library DOI: 10.1002/humu.24369 Peer reviewed articles (12) International federation of genomic medicine databases using GA4GH standards Author(s): Adrian Thorogood, Heidi L. Rehm, Peter Goodhand, Angela J.H. Page, Yann Joly, Michael Baudis, Jordi Rambla,Arcadi Navarro, Tommi H. Nyronen, Mikael Linden, Edward S. Dove, Marc Fiume, Michael Brudno, Melissa S. Cline, and Ewan Birney Published in: Cell Genomics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100032 Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants Author(s): Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo Published in: eLife, 2020, ISSN 2050-084X Publisher: eLife Sciences Publications DOI: 10.7554/elife.58705 Voices of GA4GH members: Collaborating in technology and policy development Author(s): Bartha Maria Knoppers, Danya Vears, Calvin W.L. Ho, Anna Middleton, Jacob Shujui Hsu, Alex Handler Wagner, Mélanie Courtot, Melissa Haendel, Michael Baudis, Orion Buske, Andy Yates, Kathy Reinold, Jonathan Lawson, Melissa Cline, Tiffany Boughtwood, Alexander Kanitz, Jordi Rambla, Published in: Cell Genomics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100036 GA4GH: International policies and standards for data sharing across genomic research and healthcare Author(s): Heidi L.Rehm, Angela J.H.Page, Lindsay Smith, Jeremy B.Adams, Gil Alterovitz, Lawrence J.Babb, Maxmillian P.Barkley, Michael Baudis, Michael J.S.Beauvais, Tim Beck, Jacques S.Beckmann, Sergi Beltran, David Bernick, Alexander Bernier, James K.Bonfield, Tiffany F.Boughtwood, Guillaume Bourque, Sarion R.Bowers… Ewan Birney Published in: Cell Genonics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100029 The Data Use Ontology to streamline responsible access to human biomedical datasets Author(s): Jonathan Lawson, Moran N.Cabili, Giselle Kerry, Tiffany Bought Wood, Adrian Thorogood, Pinar Alper, Sarion R.Bowers, Rebecca R.Boyles, Anthony J.Brookes, Matthew Brush, Tony Burdett, Hayley Clissold, Stacey Donnelly, Stephanie O.M.Dyke, Mallory A.Freeberg, Melissa A.Haendel, Chihiro Hata, Petr Holub, MélanieCourtot Published in: Cell Genomics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100028 GA4GH Passport standard for digital identity and access permissions Author(s): Craig Voisin, Mikael Linden, Stephanie O.M.Dyke, Sarion R.Bowers, Pinar Alper, Maxmillian P.Barkley, David Bernick, Jianpeng Chao, Mélanie Courtot, Francis Jeanson, Melissa A.Konopko, Martin Kuba, Jonathan Lawson, Jaakko Leinonen, Stephanie Li, Vivian Ota Wang, Anthony A.Philippakis, Kathy Reinold, Gregory A.Rushton, J. Dylan Spalding, Juha Törnroos, Ilya Tulchinsky, Jaime M.Guidry Auvil, Tommi Published in: Cell Genomics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100030 NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy. Author(s): Willem de Koning; Milad Miladi; Saskia Hiltemann; Astrid P. Heikema; John P. Hays; Stephan Flemming; Marius van den Beek; Dana A M Mustafa; Rolf Backofen; Björn Grüning; Andrew P. Stubbs Published in: GigaScience, Issue 2, 2020, ISSN 2047-217X Publisher: Oxford Academic DOI: 10.1093/gigascience/giaa105 Empirical validation of an automated approach to data use oversight Author(s): Moran N.Cabili, Jonathan Lawson, Andrea Saltzman, Greg Rushton, Pearl O’Rourke, John Wilbanks, Laura Lyman Rodriguez, Tommi Nyronen, Mélanie Courtot, Stacey Donnelly, Anthony A.Philippakis Published in: Cell Genomics, 2021, ISSN 2666-979X Publisher: New York: Elsevier Inc. DOI: 10.1016/j.xgen.2021.100031 Information Retrieval in an Infodemic: The Case of COVID-19 Publications Author(s): Douglas Teodoro, Sohrab Ferdowsi, Nikolay Borissov, Elham Kashani, David Vicente Alvarez, Jenny Copara, Racha Gouareb, Nona Naderi, Poorya Amini Published in: Journal of Medical Internet Research, 2021, ISSN 1438-8871 Publisher: Journal of medical Internet Research DOI: 10.2196/30161 A compendium of uniformly processed human gene expression and splicing quantitative trait loci Author(s): Nurlan Kerimov, James D. Hayhurst, Kateryna Peikova, Jonathan R. Manning,Peter Walter, Liis Kolberg, Marija Samoviča, Manoj Pandian Sakthivel, Ivan Kuzmin, Stephen J. Trevanion, Tony Burdett, Simon Jupp, Helen Parkinson, Irene Papatheodorou,Andrew D. Yates, Daniel R. Zerbino and Kaur Alasoo Published in: Nature Genetics, 2021, ISSN 1546-1718 Publisher: Nature DOI: 10.1038/s41588-021-00924-w Galactic Circos: User-friendly Circos plots within the Galaxy platform Author(s): Helena Rasche, Saskia Hiltemann Published in: GigaScience, Issue 9/6, 2020, ISSN 2047-217X Publisher: Oxford Academic DOI: 10.1093/gigascience/giaa065 Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora Author(s): Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro Published in: Frontiers in Research Metrics and Analytics, 2021, ISSN 2504-0537 Publisher: Lausanne: Frontiers Media S.A. DOI: 10.3389/frma.2021.689803 Other (18) Training Programme, Detailed D6.4 Author(s): Nicola Mulder, Mamana Mbiyavanga, Saskia Hiltemann, Vera Matser Published in: 2020 Publisher: Zenodo DOI: 10.5281/zenodo.6223125 CINECA: Catalogue of ELSI issues_D7.1 Author(s): Gennet, Éloïse; Goisauf, Melanie Published in: 2019 Publisher: Zenodo DOI: 10.5281/zenodo.3943732 CINECA_D6.1_Outreach and Dissemination Plan Author(s): Mulder, Nicola; Mbiyavanga, Mamana; Mendonca, Michelle; Matser, Vera; Hiltemann, Saskia Published in: Issue 1, 2019 Publisher: Zenodo DOI: 10.5281/zenodo.4562406 CINECA: Common Infrastructure for National Cohorts in Europe, Canada, and Africa - Kick Off Report Author(s): Keane, Thomas; Glass, Leslie Published in: 2019 Publisher: Zenodo DOI: 10.5281/zenodo.3908145 CINECA_Query expansion service_D1.2 Author(s): Tanzer, Romain; Naderi, Nona; Teodoro, Douglas; Mottaz, Anais; Ruch, Patrick; Dursi, Jonathan; Rambla de Argila, Jordi Published in: Issue 4, 2020 Publisher: Zenodo DOI: 10.5281/zenodo.4609334 CINECA Cohort Level metadata Representation D3.1 Author(s): Jin, Vivian; Brinkman, Fiona Published in: Issue 8, 2020 Publisher: Zenodo DOI: 10.5281/zenodo.4575460 CINECA_Semantic and harmonisation best practice_D3.2 Author(s): Courtot, Melanie; Liyanage, Isuru Published in: Issue 8, 2021 Publisher: Zenodo DOI: 10.5281/zenodo.5055308 CINECA Report on GA4GH Researcher ID D2.2 Author(s): Linden, Mikael; Kuba, Martin; Izquierdo, Jorge; Mbiyavanga, Mamana Published in: Issue 2, 2021 Publisher: Zenodo DOI: 10.5281/zenodo.5795408 Text mining processing pipeline for semi structured data D3.3 Author(s): Copara, Jenny; Naderi, Nona; Kellmann, Alexander; Gosal, Gurinder; Hsiao, William; Teodoro, Douglas Published in: Issue 4, 2021 Publisher: Zenodo DOI: 10.5281/zenodo.5795432 Access representation ontology developed for project's cohorts D3.5 Author(s): Courtot, Melanie; Dursi, Jonathan; Mulder, Nicola; Swertz, Morris Published in: Issue 2, 2021 Publisher: Zenodo DOI: 10.5281/zenodo.5795448 CINECA_Discovery Service Catalogue_D1.1 Author(s): Dursi, Jonathan; Rambla de Argila, Jordi; de la Torre, Sabela; Tanzer, Romain; Naderi, Nona; Mbiyavanga, Mamana; Agarwal, Samarth Published in: 2020 Publisher: Zenodo DOI: 10.5281/zenodo.3908397 CINECA_Training Programme_D6.2a Author(s): Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera Published in: 2019 Publisher: Zenodo DOI: 10.5281/zenodo.3952621 CINECA_CanDIG and ELIXIR AAI interoperability demonstration_D2.1 Author(s): Procházka, Michal; Linden, Mikael; Sethi, Amanjeev; Binsl, Thomas; Michie, Alex; Mbiyavanga, Mamana; Spalding, Dylan Published in: 2020 Publisher: Zenodo DOI: 10.5281/zenodo.3938916 CINECA Framework and APIs for executing federated genomics analyses D4.2 Author(s): Álvaro González, Shubham Kapoor, Kirill Tsukanov Published in: 2020 Publisher: Zenodo DOI: 10.5281/zenodo.4609356 Catalogue of Canadian, European and African ethical and legal gaps Author(s): Gennet, ��lo��se; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle Published in: Issue 1, 2020 Publisher: Zenodo DOI: 10.5281/zenodo.4298449 CINECA: Data Management Plan v.1 Author(s): Kerry, Giselle; Glass, Leslie; Keane, Thomas; Ruch, Patrick; Mulder, Nicola; Brinkman, Fiona Published in: 2019 Publisher: Zenodo DOI: 10.5281/zenodo.3909577 Training Programme_Annual Report 2021 D6.5 Author(s): Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera; Lloret Llinares, Marta Published in: Issue 4, 2021 Publisher: Zenodo DOI: 10.5281/zenodo.5795482 CINECA: Report on trust model for partner sites, and between sites and controlled-access researchers Author(s): Cirillo, Elisa; Alasoo, Kaur; Michie, Alex; Binsl, Thomas; Törnroos, Juha; Kapoor, Shubham; Tsukanov, Kirill; Rayner, William; Mbiyavanga, Mamana; Rashid, Shaikh; Westra, Harm-Jan Published in: 2020 Publisher: Zenodo DOI: 10.5281/zenodo.3909521 Searching for OpenAIRE data... 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