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

Risultati finali

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).

First recommendations needed for implementation implemented in IT Framework (incl. a Data Management Plan)

First recommendations needed for implementation implemented in IT Framework We will provide recommendations for the longterm cooperation between European African and Canadian cohorts to intensify collaboration as well as sharing and reuse of data56 ethical and legal recommendations IT solutions such as machine readable solutions to meet ethical and legal requirements and vice versa

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

Report of main achievements, impacts, sustainability and exploitation

Report of main achievements impacts sustainability and exploitation

Meta-analysis of splicing and expression QTLs across three cohorts

A Metaanalysis of splicing and expression QTLs across three cohorts We willdevelop a federated metaanalysis protocol that complies with the data sharing and privacy requirements of the individual cohorts and apply it to the three cohorts participating in the implementation study BIOS EGCUT TwinsUK Finally in collaboration with the eQTL Catalog currently being developed at EMBLEBI and UTartu we will make summary statistics from the federated eQTL metaanalysis available via public APIs

Report of impact and key results

Development of a sustainability plan of each project result for maximum longterm 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.

Data interoperability documentation

An important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42

Integration of new cohort infrastructures to the ELIXIR AAI

A report with the status of integration of new service providers to the ELIXIR AAI Due to the federated nature of human data each infrastructure has their own processes and procedures for granting access to datasets hosted We are proposing to harmonise AAI across the CINECA consortium by ensuring that all of the cohort infrastructures are integrated with either ELIXIR or CanDIG AAI or H3Africa

Curation-support for care planning

Curationsupport for care planning with the aim to add clinical actionability beyond pathogenicity scales

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.

Development and application of optimised polygenic risk scores

A report on the development and application of optimised polygenic risk scores We will focus on the development and implementation of methods to generate polygenic risk scores for traits of mutual interest and to use them both for trait prediction and causal inference in a Mendelian randomisation framework The methods developed will generate novel biological and translational insights including polygenic risk scores for medically relevant traits such as type 2 diabetes and coronary artery disease that are optimised for use across multiple samples andor populations

Final report and impact analysis

A final report and impact analysis Summary report of all outreach dissemination and training activities including impact analysis

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

Populated minimal meta data model for project cohorts

A minimal meta data model will provide a common for data discovery WP1 and will be populated by data from each cohort enabling federated analyses WP4 and clinical applications WP5

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.

Federated discovery across registry services

An important use case of the federated discovery services is to discover cohorts of relevant samples or patients across data providers either programmatically or with interactive tools such as the portal of T141 and run uniform pipelines across those items for further analysis with the tools of T42

Pubblicazioni

CINECA - Meta-analysis of splicing and expression QTLs across three cohorts D4.4

Autori: Alasoo, Kaur; Warmerdam, Robert; Westra, Harm-Jan
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7464116

Training Programme, Detailed D6.4

Autori: Nicola Mulder, Mamana Mbiyavanga, Saskia Hiltemann, Vera Matser
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.6223125

CINECA Report of main achievements, impacts, sustainability and exploitation D8.4

Autori: Garcia, Carles
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8099739

CINECA: Catalogue of ELSI issues_D7.1

Autori: Gennet, Éloïse; Goisauf, Melanie
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3943732

CINECA Catalogue of Canadian, European and African ethical and legal gaps D7.2

Autori: Gennet, Éloïse; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.6256295

Systematic visualisation of molecular QTLs reveals variant mechanisms at GWAS loci

Autori: 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
Pubblicato in: BioRxiv, 2023
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.04.06.535816

CINECA Data interoperability documentation D1.4

Autori: Spalding, Dylan
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8093973

CINECA_D6.1_Outreach and Dissemination Plan

Autori: Mulder, Nicola; Mbiyavanga, Mamana; Mendonca, Michelle; Matser, Vera; Hiltemann, Saskia
Pubblicato in: Issue 1, 2019
Editore: Zenodo
DOI: 10.5281/zenodo.4562406

CINECA: Common Infrastructure for National Cohorts in Europe, Canada, and Africa - Kick Off Report

Autori: Keane, Thomas; Glass, Leslie
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3908145

CINECA Integration of new cohort infrastructures to the ELIXIR AAI - D2.3

Autori: Licehammer; Bučík; Broncová; Spalding
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8056340

CINECA Federated Data Analytics for European Biobanks D5.1

Autori: Ruch; Mottin; Michel; Pasche; Mottaz; Naderi
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.6783295

CINECA_Query expansion service_D1.2

Autori: Tanzer, Romain; Naderi, Nona; Teodoro, Douglas; Mottaz, Anais; Ruch, Patrick; Dursi, Jonathan; Rambla de Argila, Jordi
Pubblicato in: Issue 4, 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4609334

CINECA Cohort Level metadata Representation D3.1

Autori: Jin, Vivian; Brinkman, Fiona
Pubblicato in: Issue 8, 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4575460

CINECA Populated minimal metadata model for project cohorts - D3.4

Autori: Brinkman, Fiona
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8297040

CINECA_Semantic and harmonisation best practice_D3.2

Autori: Courtot, Melanie; Liyanage, Isuru
Pubblicato in: Issue 8, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5055308

CINECA Federated discovery across registry services D1.3

Autori: Fromont; Milla
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8099693

CINECA Report on GA4GH Researcher ID D2.2

Autori: Linden, Mikael; Kuba, Martin; Izquierdo, Jorge; Mbiyavanga, Mamana
Pubblicato in: Issue 2, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5795408

CINECA D7.3 First recommendations for implementation in IT Framework (Incl. a Data Management Plan)

Autori: Goisauf, Melanie; Fériol, Lisa; Rial-Sebbag, Emmanuelle
Pubblicato in: 2022
Editore: Zenodo
DOI: 10.5281/zenodo.7680755

Text mining processing pipeline for semi structured data D3.3

Autori: Copara, Jenny; Naderi, Nona; Kellmann, Alexander; Gosal, Gurinder; Hsiao, William; Teodoro, Douglas
Pubblicato in: Issue 4, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5795432

Access representation ontology developed for project's cohorts D3.5

Autori: Courtot, Melanie; Dursi, Jonathan; Mulder, Nicola; Swertz, Morris
Pubblicato in: Issue 2, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5795448

CINECA GDPR and FAIR compliant Diagnostic Services D5.3

Autori: Johansson, Lennart; Been, Gerieke; Michie, Alex; Binsl, Thomas
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7925804

CINECA_Discovery Service Catalogue_D1.1

Autori: Dursi, Jonathan; Rambla de Argila, Jordi; de la Torre, Sabela; Tanzer, Romain; Naderi, Nona; Mbiyavanga, Mamana; Agarwal, Samarth
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3908397

CINECA_Training Programme_D6.2a

Autori: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3952621

CINECA Universal FAIR Data Compliant Federated Biomarker Discovery Service D5.2

Autori: Hiltemann, Saskia; Ouwerkerk, Jasper; Stubbs, Andrew
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7925781

CINECA Data Management Plan v2

Autori: Glass, Leslie; Spalding, Dylan; Mulder, Nicola; Courtot, Melanie; Brinkman, Fiona; Ruch, Patrick
Pubblicato in: 2021
Editore: Zenodo
DOI: 10.5281/zenodo.4683415

CINECA_CanDIG and ELIXIR AAI interoperability demonstration_D2.1

Autori: Procházka, Michal; Linden, Mikael; Sethi, Amanjeev; Binsl, Thomas; Michie, Alex; Mbiyavanga, Mamana; Spalding, Dylan
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3938916

CINECA Framework and APIs for executing federated genomics analyses D4.2

Autori: Álvaro González, Shubham Kapoor, Kirill Tsukanov
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4609356

CINECA Curation-support application for care planning D5.4

Autori: Ruch, Patrick; Naderi, Nona; Mottin, Luc; Pasche, Emilie; Mottaz, Anais
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7925825

Catalogue of Canadian, European and African ethical and legal gaps

Autori: Gennet, ��lo��se; Goisauf, Melanie; Pichereau, Delphine; Rial-Sebbag, Emmanuelle
Pubblicato in: Issue 1, 2020
Editore: Zenodo
DOI: 10.5281/zenodo.4298449

CINECA Risk Management Registry D8.2

Autori: Keane, Thomas
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.7734061

CIENCA Final Report and Impact Analysis D6.3

Autori: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Gurwitz, Kim; Lloret Llinares, Marta; Thomas Lopez, Daniel
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.7925741

CINECA Report of impact and key results D8.3

Autori: Garcia, Carles
Pubblicato in: 2023
Editore: Zenodo
DOI: 10.5281/zenodo.8099814

CINECA: Data Management Plan v.1

Autori: Kerry, Giselle; Glass, Leslie; Keane, Thomas; Ruch, Patrick; Mulder, Nicola; Brinkman, Fiona
Pubblicato in: 2019
Editore: Zenodo
DOI: 10.5281/zenodo.3909577

Training Programme_Annual Report 2021 D6.5

Autori: Mulder, Nicola; Mbiyavanga, Mamana; Hiltemann, Saskia; Matser, Vera; Lloret Llinares, Marta
Pubblicato in: Issue 4, 2021
Editore: Zenodo
DOI: 10.5281/zenodo.5795482

CINECA: Report on trust model for partner sites, and between sites and controlled-access researchers

Autori: Cirillo, Elisa; Alasoo, Kaur; Michie, Alex; Binsl, Thomas; Törnroos, Juha; Kapoor, Shubham; Tsukanov, Kirill; Rayner, William; Mbiyavanga, Mamana; Rashid, Shaikh; Westra, Harm-Jan
Pubblicato in: 2020
Editore: Zenodo
DOI: 10.5281/zenodo.3909521

Reconciling the biomedical data commons and the GDPR: three lessons from the EUCAN ELSI collaboratory

Autori: 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
Pubblicato in: European Journal of Human Genetics, 2023, ISSN 1476-5438
Editore: Nature
DOI: 10.1038/s41431-023-01403-y

International federation of genomic medicine databases using GA4GH standards

Autori: 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
Pubblicato in: Cell Genomics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100032

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants

Autori: Liis Kolberg, Nurlan Kerimov, Hedi Peterson, Kaur Alasoo
Pubblicato in: eLife, 2020, ISSN 2050-084X
Editore: eLife Sciences Publications
DOI: 10.7554/elife.58705

Assessing the use of supplementary materials to improve genomic variant discovery

Autori: Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch
Pubblicato in: Database, Issue Volume 2023, 2023, ISSN 1758-0463
Editore: Oxford University Press
DOI: 10.1093/database/baad017

Voices of GA4GH members: Collaborating in technology and policy development

Autori: 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,
Pubblicato in: Cell Genomics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100036

GA4GH: International policies and standards for data sharing across genomic research and healthcare

Autori: 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
Pubblicato in: Cell Genonics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100029

The Data Use Ontology to streamline responsible access to human biomedical datasets

Autori: 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
Pubblicato in: Cell Genomics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100028

GA4GH Passport standard for digital identity and access permissions

Autori: 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
Pubblicato in: Cell Genomics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100030

Training Infrastructure as a Service

Autori: 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
Pubblicato in: Gigascience, Issue 2022 Dec 28;12:giad048, 2023, ISSN 2047-217X
Editore: Oxford Academy
DOI: 10.1093/gigascience/giad048

NanoGalaxy: Nanopore long-read sequencing data analysis in Galaxy.

Autori: 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
Pubblicato in: GigaScience, Issue 2, 2020, ISSN 2047-217X
Editore: Oxford Academic
DOI: 10.1093/gigascience/giaa105

Empirical validation of an automated approach to data use oversight

Autori: 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
Pubblicato in: Cell Genomics, 2021, ISSN 2666-979X
Editore: New York: Elsevier Inc.
DOI: 10.1016/j.xgen.2021.100031

Information Retrieval in an Infodemic: The Case of COVID-19 Publications

Autori: Douglas Teodoro, Sohrab Ferdowsi, Nikolay Borissov, Elham Kashani, David Vicente Alvarez, Jenny Copara, Racha Gouareb, Nona Naderi, Poorya Amini
Pubblicato in: Journal of Medical Internet Research, 2021, ISSN 1438-8871
Editore: Journal of medical Internet Research
DOI: 10.2196/30161

A compendium of uniformly processed human gene expression and splicing quantitative trait loci

Autori: 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
Pubblicato in: Nature Genetics, 2021, ISSN 1546-1718
Editore: Nature
DOI: 10.1038/s41588-021-00924-w

Galactic Circos: User-friendly Circos plots within the Galaxy platform

Autori: Helena Rasche, Saskia Hiltemann
Pubblicato in: GigaScience, Issue 9/6, 2020, ISSN 2047-217X
Editore: Oxford Academic
DOI: 10.1093/gigascience/giaa065

Ensemble of deep learning language models to support the creation of living systematic reviews for the COVID-19 literature

Autori: Julien Knafou, Quentin Haas, Nikolay Borissov, Michel Counotte , Nicola Low, Hira Imeri, Aziz Mert Ipekci, Diana Buitrago-Garcia, Leonie Heron, Poorya Amini, Douglas Teodoro
Pubblicato in: Systematic Reviews, Issue Systematic Reviews 12, Article number: 94 (2023), 2023, ISSN 2046-4053
Editore: 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

Autori: 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
Pubblicato in: Human Mutation, Issue 2022 Jun;43(6), 2022, Page(s) 791-799, ISSN 1098-1004
Editore: Wiley Online Library
DOI: 10.1002/humu.24369

Ensemble of Deep Masked Language Models for Effective Named Entity Recognition in Health and Life Science Corpora

Autori: Nona Naderi, Julien Knafou, Jenny Copara, Patrick Ruch, Douglas Teodoro
Pubblicato in: Frontiers in Research Metrics and Analytics, 2021, ISSN 2504-0537
Editore: Lausanne: Frontiers Media S.A.
DOI: 10.3389/frma.2021.689803

Designing an Optimal Expansion Method to Improve the Recall of a Genomic Variant Curation-Support Service

Autori: Anaïs Mottaz, Emilie Pasche, Pierre-André Michel, Luc Mottin, Douglas Teodoro, Patrick Ruch
Pubblicato in: Studies in Health Technology and Informatics, Issue Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Page(s) 839 - 843
Editore: IOS Press
DOI: 10.3233/shti220603

Analyzing the Information Content of Text-Based Files in Supplementary Materials of Biomedical Literature

Autori: Nona Naderi, Anaïs Mottaz, Douglas Teodoro, Patrick Ruch
Pubblicato in: Studies in Health Technology and Informatics, Issue Volume 294: Challenges of Trustable AI and Added-Value on Health, 2022, Page(s) 876 - 877
Editore: IOS Press
DOI: 10.3233/shti220614

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