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

3.5 hr = 1' 40'' session + 10'' break + 1' 30'' session

210

20+20+45=85

Agenda

Welcome and introduction: Kavi (15 minutes) 1pm -120pm

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

20,000 feet view: Shawn (20 mins) (slides)  120pm-2pm

Data Model and Query Tool:  Jeff (40 minutes) 2pm-240p, 

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. Methods of installation
2. Synthea on ACT Ontology with COVID19
3. SHRINE 3 node with HUB Instal
4. Exercise 4

BREAK (15 minutes)

ETL pipeline for i2b2: Kavi (40 minutes) + QA 10 mins  Slides 

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 varied 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

Summary: Shawn 10 mins (slides)