a retrieval information system for medical research Convergence with I2B2
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1 a retrieval information system for medical research Convergence with I2B2 Marc Cuggia & Nicolas Garcelon Inserm U936 Rennes Fondation Imagine - Paris
2 Objective of Roogle project To develop a global retrieval information system for medical research Dealing with freetext and coded data Providing tools to select patients or cohort Quite similar to existing tools (I2B2, Stride, Archimed)
3 Goal of the presentation To present Roogle from a technical functional point of view To imagine how Roogle could interact with I2B2
4 Technical aspect of Roogle (1) Web tool Languages :PHP, Ajax Database : Oracle Oracle Text Oracle Geolocation ETL : Perl scripts / Talend Terminology system : UMLS
5 Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
6 Search engine data Annotation Terminologies Manager Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
7 WORKBENCH Builder Structured Temporal Free Text Combi Criteria Search engine data Annotation Terminologies Manager Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
8 WORKBENCH Builder Structured Temporal Free Text Combi Criteria Statistics & working lists Result Visualization data Time Line Geo location Legacy EHR Access De-ID Tool Search engine data Annotation Terminologies Manager Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
9 WORKBENCH Structured Temporal Builder Free Text Combi Criteria Basket Manager Statistics & working lists Selection tool Gestion inclusion/exclu sion Datamart Manager Result Visualization data Time Line Import/Export Data tool Geo location Legacy EHR Access De-ID Tool Search engine data Annotation Terminologies Manager Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
10 WORKBENCH Study request manager Study Manager Workflow Communication Study Dashboard «Non consent to be recontacted» registry User Manager User Directory Structured Temporal Builder Free Text Combi Criteria Basket Manager Statistics & working lists Selection tool Gestion inclusion/exclu sion Datamart Manager Result Visualization data Time Line Import/Export Data tool Geo location Legacy EHR Access De-ID Tool Search engine data Annotation Terminologies Manager Audit trail CRON LOAD TRANSFORM EXTRACT Semantic services (Annotation) Negation Expansion EHR Lab RIS Pathologie DRG Hospital Information System registry
11 Functional description Demo Roogle Example taken from a realistic clinical trial Find patients with the following criteria : Inclusion + Age : 30 to 90 years + Finding : dyskinesia + Drugs : rasagiline or selegiline or deprenyl or Otrasel or LDopa + Diagnosis : parkinson disease Exclusion - Diagnosis : hypertension
12 Converging with I2B2 I2B2 is becoming a standard in with a modular approach (Hive - cells) supported by a large community of developers How to take benefit of I2B2 & Roogle?
13 Scenario 1 Roogle as workbench on I2B2 DATABASE
14 Scenario 2 Roogle as Shrine and I2B2 as an endpoint Pivot model (information/term) Semantic service Mapping service MEDIATOR Orchestrator Site registry Security Audit Trail Crypt/decrypt Approb
15 Scenario 3 Roogle modules as re-usable components in the I2B2 Hive. Semantic enrichment Geo Location Selection De-ID
16 Conclusion Roogle is an information retrieval system for medical research Currently used in 3 academic hospitals Planned to be deployed in 20 cancer hospitals in France Roogle & I2B2 could have some point of converge with different strategies
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