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Common Infrastructure for National Cohorts in Europe, Canada, and Africa

Deliverables

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).

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.

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

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.

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Publications

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, 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, 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

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: 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: 4, 2020
Publisher: Zenodo
DOI: 10.5281/zenodo.4609334

CINECA Cohort Level metadata Representation D3.1

Author(s): Jin, Vivian; Brinkman, Fiona
Published in: 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: 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: 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: 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: 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: 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: 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