THE MIRACUM CONSORTIUM

Transcription

1 THE MIACUM CONSOTIUM Prof. Dr. Hans-Ulrich Prokosch Chair of Medical Informatics, University of Erlangen-Nürnberg CIO University Hospital Erlangen MIACUM Coordinator Meeting with EHDEN consortium members / Mannheim 1

2 Medical Informatics for esearch and Care in University Medicine

3 MIACUM will be (9+/2018)... the largest MII Consortium ten (eleven) University Hospitals & Medical Faculties two universities for applied science one industrial partner (Averbis GmbH) handling clinical and research data of more than 12 million patients 1

4 MIACUM DIC Architecture Clinical Module ID-/Consent-Management esearch Module outine business intelligence Consent- Management esearch queries Source system 1 Harmonization Comm- Server Source system 2 Clinical data repository NLP esearch data repository esearch data longterm archive Clinical Decision Support Local ID- Management Federation 4

5 The MIACUM Ecosystem 1. Medical Informatics eusable ecosystem of Open source Linkable and Interoperable software tools X MIACOLIX 2. MIACOLIX is pragmatic modular reusable open source interoperable federated 5

6 Areas of Development epositories Integration Tools Project & Trial Management IT- Infrastructure Protection 6

7 Areas of Development Integration Tools IT- Infrastructure epositories Protection Project & Trial Management epositories, Exploration & Visualization i2b2 & IDT Tools transmat CDM & OHDSI Tools XNAT cbioportal Long-Term esearch Archive iods CKAN 7

8 Areas of Development MIACUM Metadata epository based on Samply.MD epositories ETL Tools Integration Tools Project & Trial Management Harmonisation/Mapping Tool Erlangen Ontology-based Mapping Tools based on GBA / BBMI EIC CS IT tools MOLGENIS (BiobankConnect) IT- Infrastructure Protection Natural Language Processing Tool Averbis Information Discovery Tool Connector Components required for the federated network of DICs based on i2b2, Samply Broker/Connector, Arachne 8

9 Areas of Development epositories Federated Authentication oauth Accounts issued in home institutions can be used via DFN-AAI Integration Tools Project & Trial Management Tools for Development, Deployment and Monitoring of IT Solutions IT- Infrastructure Protection Sharing and Deployment of Software Pipelines for Analysis of OMICs to share, use, and learn to compare the different results and to build the ground for the definition of quality parameters and requirements Galaxy, Galaxy Tool Shed & Docker 9

10 Areas of Development epositories Project Proposal Management Atlassian Confluence ProSKIVE Integration Tools IT- Infrastructure Protection Project & Trial Management Hospital-/Faculty-wide Trial- /Project egistry Includes all relevant metadata including eligibility criteria ( recruitment tool) based on prototypes existing in Erlangen, Frankfurt, and Freiburg 10

11 Areas of Development epositories ID-Management Tool Mainzelliste Integration Tools Project & Trial Management Anonymization Tool e.g. AX ( IT- Infrastructure Protection Consent Management Tool gics (generic informed consent service) 11

12 Areas of Development Integration Tools IT- Infrastructure epositories Community Management Protection Project & Trial Management All developments will be available original work & customizations under decision: github, gitlab, bitbucket All developments will be supported Community fora, mailinglists, slack,... 12

13 Strategy Lead partner per component: MIACUM Competence Center Based on experience e.g. Erlangen for i2b2, Freiburg for galaxy, Magdeburg for XNAT gives support to others in setting up the component locally receives support in setting up the other components locally Strong community

14 MIACUM DIC Architecture and data protection Clinical Module ID-/Consent-Management esearch Module outine business intelligence Consent- Management esearch queries Source system 1 Harmonization Comm- Server Source system 2 Clinical data repository NLP esearch data repository esearch data longterm archive Clinical Decision Support Local ID- Management Federation 14

15 MIACUM DIC Architecture and data protection Protection Concept Version 0.8 was positively voted by the bavarian data protection officer Based on our strictly federated approach for feasibility studies (federated cohort identification) federated analysis 15

16 MIACUM DIC 0.9 pilot data integration during the conceptual phase Source data 21 Core Set Person, Case, Demographics, Integrated epository Toolkit ETL IDT Talend Diagnosis, Procedures epository i2b2 Standardized German billing data set Queries SQL SQL no data harmonization required Federation L-i2b2 Pilot Architecture

17 MIACUM Federated Analysis Bring the analysis to the data Erlangen Frankfurt Freiburg Gießen -Script SQL- Statement Magdeburg Mainz Mannheim Marburg 5

18 MIACUM Federated Analysis Bring the analysis to the data Erlangen Frankfurt Freiburg Gießen -Script SQL- Statement Magdeburg Mainz Mannheim Marburg 5

19 MIACUM Federated Analysis Bring the analysis to the data Erlangen Frankfurt Freiburg Gießen Proof-of-Concept Analysis: -Script aggregated results SQL- Statement Stroke / Thrombectomy Analysis of Guideline Adherence Colorectales Cancer Analysis of Therapy Patterns Magdeburg Mainz Mannheim Marburg 5

20 First Analysis and Publications Combined Sunburst-Plot of Treatment-Pathways for 18,376 patients with colorecal cancer from 11 hospitals 20

21 First Analysis and Publications 21

22 The NSC demonstrator study Applying this federated approach (based on our i2b2 Docker provision) a demonstrator study is currently planned with partners from all consortia The research questions of this demonstrator study focus on Multimobidity are Diseases 22

23 MIACUM Use Cases IT supported patient recruitment for clinical trials Phenotyping Querying EH database / DIC data repositories Prediction Models for COPD/Asthma and Brain Cancer Patients Federated machine learning Prediction Model Deployment SMAT App Integration in EH environments Supporting Precision Medicine in Moleculare Tumorboards bioinformatics pipelines (e.g. Galaxy) integration of clinical and genomic data (e.g. cbioportal) 23

24 MIACUM Summer School esearch and Teaching MIACUM Summer School 29. July 03. August 2018 Alsace (France) Medical (esearch) Informatics Essentials Prof. Dr. James Cimino Director of Informatics Institute The University of Alabama at Birmingham, USA

25 MIACUM Seminar esearch and Teaching

26 My thanks to our MIACUM Team... and for your interest Förderkennzeichen: 01ZZ1801A