Page History
Saturday Nov 14, 2020 ; 2-5:30pm (3.5 hours)
Agenda
Welcome and introduction: Kavi (10 minutes)
- Workspaces for Hands-on exercises (video)
- Participant Survey
20,000 feet view: Shawn (20 mins) (slides)
Data Model and Query Tool: Jeff (45 minutes) + QA 10
- Intro to i2b2
- Query Tool
- Ontologies
- Data Model
- Community Project Highlights (ACT, genomics, etc. Medco?) - i2b2 on OMOP / OMOP to i2b2
- Exercise 1: Building a query (demo data) [15 minutes]
- Ontology Browser
- Find Terms
- Counts Query
- Breakdown
- Exercise 2: Building a temporal query (demo data) [10 minutes]
- Exercise 3: Export some data (export XLS ) [10 minutes]
Installation and Shrine: Mike (45 minutes) + QA 10 mins
- Methods of installation
- Synthea on ACT Ontology with COVID19
- SHRINE 3 node with HUB Instal
- Exercise 4
BREAK (15 minutes)
Q and A (15 minutes)
ETL pipeline for i2b2: Kavi (40 minutes) + QA 10 mins Slides
- Exercise 5: Create and upload simple concept ontology and facts: (video)
- Exercise 6: Create and upload concepts with varied data-types (video)
- How i2b2 is helpful for lab level projects:
- Enforces data dictionary & discipline
- Query tool validates SQL for reporting
Summary: Shawn 10 mins (slides)