Selected article for: "Data analysis and open source"
Author: Gabriel A Brat; Griffin M Weber; Nils Gehlenborg; Paul Avillach; Nathan P Palmer; Luca Chiovato; James Cimino; Lemuel R Waitman; Gilbert S Omenn; Alberto Malovini; Jason H Moore; Brett K Beaulieu-Jones; Valentina Tibollo; Shawn N Murphy; Sehi L'Yi; Mark S Keller; Riccardo Bellazzi; David A Hanauer; Arnaud Serret-Larmande; Alba Gutierrez-Sacristan; John J Holmes; Douglas S Bell; Kenneth D Mandl; Robert W Follett; Jeffrey G Klann; Douglas A Murad; Luigia Scudeller; Mauro Bucalo; Katie Kirchoff; Jean Craig; Jihad Obeid; Vianney Jouhet; Romain Griffier; Sebastien Cossin; Bertrand Moal; Lav P Patel; Antonio Bellasi; Hans U Prokosch; Detlef Kraska; Piotr Sliz; Amelia LM Tan; Kee Yuan Ngiam; Alberto Zambelli; Danielle L Mowery; Emily Schiver; Batsal Devkota; Robert L Bradford; Mohamad Daniar; Christel Daniel; Vincent Benoit; Romain Bey; Nicolas Paris; Patricia Serre; Nina Orlova; Julien Dubiel; Martin Hilka; Anne Sophie Jannot; Stephane Breant; Judith Leblanc; Nicolas Griffon; Anita Burgun; Melodie Bernaux; Arnaud Sandrin; Elisa Salamanca; Thomas Ganslandt; Tobias Gradinger; Julien Champ; Martin Boeker; Patricia Martel; Alexandre Gramfort; Olivier Grisel; Damien Leprovost; Thomas Moreau; Gael Varoquaux; Jill Jen Vie; Demian Wassermann; Arthur Mensch; Charlotte Caucheteux; Christian Haverkamp; Guillaume Lemaitre; Christian Haverkamp; Tianxi Cai; Isaac S Kohane
Title: International Electronic Health Record-Derived COVID-19 Clinical Course Profile: The 4CE Consortium
  • Document date: 2020_4_18
    • ID: 4y5279c5_10
    Snippet: Sites obtained the data for their files in several ways. Most sites leveraged the open source i2b2 software platform already installed at their institution 20 which supports query and analysis of clinical and genomics data. More than 200 organizations worldwide use i2b2 for a variety of purposes, including identifying patients for clinical trials, drug safety monitoring, and epidemiology research. Most 4CE sites with i2b2 used database scripts to.....
    Document: Sites obtained the data for their files in several ways. Most sites leveraged the open source i2b2 software platform already installed at their institution 20 which supports query and analysis of clinical and genomics data. More than 200 organizations worldwide use i2b2 for a variety of purposes, including identifying patients for clinical trials, drug safety monitoring, and epidemiology research. Most 4CE sites with i2b2 used database scripts to directly query their i2b2 repository to calculate counts needed for data files. Institutions without i2b2 used their own clinical data warehouse solutions and querying tools to create the files. In some cases, a hybrid method was used that leveraged different data warehouse platforms to fill in i2b2 gaps. For example, Assistance Publique -Hôpitaux de Paris (APHP), the largest hospital system in Europe, aggregates all EHR data from 39 hospitals in Paris and its surroundings. APHP exported data from the Observational Medical Outcomes Partnership (OMOP) Common Data Model for transformation to the shared format.

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