2 nd European i2b2 AUG Meeting The Integrated Data Repository Toolkit (IDRT) Platform Architecture And Tools to Support The Re-use of Routine Clinical Data For Research Christian Bauer (presenter), Benjamin Baum, Igor Engel, Thomas Ganslandt, Matthias Löbe, Sebastian Mate, Hans-Ulrich Prokosch, Matthias Quade, Ulrich Sax, Sebastian Stäubert, Alfred Winter Contact: idrt@imise.uni-leipzig.de Website: idrt.imise.uni-leipzig.de TMF - Technologie und Methodenplattform für die vernetzte medizinische Forschung e. V.
IDRT: Goals source data source data terminologies? ID management i2b2 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 2
IDRT: First Project Phase Easy installation and configuration of i2b2 (i2b2 Wizard) Easy import of study and clinical data (IDRT Import Tool) Easy import of (german) terminologies (IDRT Import Tool) Terminologien Studiendaten 10.09. Trial Data CDISC ODM klinische Daten Clinical Data CSV/SQL Terminologies IDRT Import Tool i2b2 i2b2 Wizard 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 3
IDRT: i2b2 Wizard Full i2b2 installation support Automatic download and installation of required software packages Automatic handling of all database work (schema creation, etc.) Full support for i2b2 administration Handling of i2b2 projects, users, server status etc. 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 4
IDRT: IDRT Import Tool Local Java-RCP application with a i2b2 project browser for importing CDISC-ODM, CSV/SQL, Terminologies, 21 data 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 5
IDRT: IDRT Import Tool Local Java-RCP application with a i2b2 project browser for importing CDISC-ODM, CSV/SQL, Terminologies, 21 data 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 6
IDRT: IDRT Import Tool Local Java-RCP application with a i2b2 project browser for importing CDISC-ODM, CSV/SQL, Terminologies, 21 data 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 7
IDRT: IDRT Import Tool ETL based on Talend Open Studio 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 8
IDRT2: Second Project Phase Goals of the second project phase Updating and expanding the i2b2 Wizard / IDRT Import Tool Adding an editor for rearanging and enriching i2b2-ontologies Adding support of i2b2-modifiers to enable more complex queries Database optimization strategies 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 9
IDRT2: i2b2 Wizard Integration of SHRINE Update for i2b2 1.7 (backward compatible) Installation of i2b2-webclient-plugins Modular design: use different components for individual needs: i2b2 version / operating system (Ubuntu/CentOS/Windows with Cygwin) / database (Oracle/MSSql/Postgres) / Jboss / Ant 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 10
IDRT2: IDRT Import Tool New import sources Biomaterial (starlims) German National Metadata Repository (based on ISO/IEC 11179) 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 11
IDRT2: i2b2-ontology-editor Trial Data CDISC ODM klinische Daten Clinical Data CSV/SQL IDRT Import i2b2 Terminologien Studiendaten Terminologies 10.09. i2b2 Wizard 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 12
IDRT2: i2b2-ontology-editor Terminologien Trial Data CDISC ODM klinische Daten Clinical Data CSV/SQL IDRT Import i2b2 staging IDRT IOE i2b2 Studiendaten Terminologies 10.09. i2b2 Wizard 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 13
IDRT2: i2b2-ontology-editor 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 14
IDRT2: i2b2-ontology-editor i2b2 Staging i2b2 Target 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 15
IDRT2: i2b2-ontology-editor 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 16
IDRT2: i2b2-ontology-editor Functions: Copy, Rename Rearrange, create new items/folders Map Items Dates Terminologies 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 17
IDRT2: i2b2-ontology-editor Copy patient data 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 18
IDRT2: i2b2-ontology-editor Mapping/merging patient data with ICD classification 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 19
IDRT2: i2b2-ontology-editor patient data ICD 10 with patient data ICD 10 classification structure and codes 10.09.2014 Christian Bauer - christian.bauer@med.uni-goettingen.de 20 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 20
IDRT2: i2b2-modifiers i2b2-modifier allow to bundle multiple patient data facts for a group of items i2b2-modifiers support added to CDISC-ODM import: Repeating Elements CSV/SQL import: use whole file/table as i2b2-modifier subtree i2b2-ontology-editor Created i2b2 webclient plugin 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 21
IDRT2: i2b2-modifiers i2b2 concepts: search for all male patients (give age), who i2b2 modifier path 1: have a father or brother with diagnose X1, X2 or X3 and i2b2 modifier path 2: have specimen (give specimen ID and storage location) 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 22
IDRT2: IDRT webclient plugin i2b2 concept results as plain table 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 23
New: Modifier Webclient Plugin i2b2 concept results as plain table i2b2 modifier results are bundled by paths into tabs 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 24
New: Modifier Webclient Plugin i2b2 concept results as plain table i2b2 modifier results are bundled by paths into tabs all results can be merged in one table 2nd EU AUG, Göttingen 11.09.2014 christian.bauer@med.uni-goettingen.de Page 25
2nd European i2b2 AUG Meeting The Integrated Data Repository Toolkit (IDRT) Platform Architecture And Tools to Support The Re-use of Routine Clinical Data For Research Christian Bauer (presenter), Benjamin Baum, Igor Engel, Thomas Ganslandt, Matthias Löbe, Sebastian Mate, Hans-Ulrich Prokosch, Matthias Quade, Ulrich Sax, Sebastian Stäubert, Alfred Winter Contact: idrt@imise.uni-leipzig.de Website: idrt.imise.uni-leipzig.de TMF - Technologie und Methodenplattform für die vernetzte medizinische Forschung e. V.