links ( bit.do/i2b2amia )

1. workspace

2. interaction

October 30, 2021 from 1:00 PM to 4:30 PM

Agenda

Details

Welcome and introduction: Kavi 

1. Workspaces for Hands-on exercises  (video)
2. Participant Introduction 

20,000 feet view: Shawn (20 mins) (slides)  

Data Model and Query Tool:  Jeff  

1. Intro to i2b2
   1. Query Tool
   2. Ontologies 
   3. Data Model
   4. Community Project Highlights (ACT, genomics, etc. Medco?) - i2b2 on OMOP / OMOP to i2b2
2. Exercise 1: Building a query (demo data) [15 minutes]
   1. Ontology Browser
   2. Find Terms
   3. Counts Query
   4. Breakdown
3. Exercise 2: Building a temporal query (demo data) 
4. Exercise 3: Export some data (export XLS ) 

Installation and Shrine:  Mike (45 minutes) + QA 10 mins

1. Synthea data
2. ACT Ontology with COVID19
3. linking i2b2 to OMOP database

BREAK (15 minutes)

ETL pipeline for i2b2: Kavi 

1.  Exercise 5: Create and upload simple concept ontology and facts: (video)
   1. Files:
      1. ex5_concepts.csv
      2. ex5_facts.csv
2.  Exercise 6: Create and upload concepts with various data-types (video)
   1. Files
      1. ex6_concepts.csv
      2. ex6_facts.csv
3. How i2b2 is helpful for lab level projects:
   1. Enforces data dictionary & discipline
   2. Query tool validates SQL for reporting

workshop Team projects