Saturday Nov 14, 2020 ; 2-5:30pm  (3.5 hours)

Before session:

• online handouts
• demo accounts

Agenda

Welcome and introduction: Kavi (10 minutes)

1. user-access 
2. Survey: why they are doing this tutorial 

Big picture: Shawn 20 mins

Data Model and Query Tool:  Jeff (40 minutes) + QA 10 

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) [10 minutes]
4. Exercise 3: Export some data (export XLS or Nich’s pt set plugin) [10 minutes]

Installation and Shrine:  Mike (40 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
5. FAQ

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

1.  Exercise 5: Create and upload simple concept ontology and facts:
   1. Files: concept.csv fact.csv
2.  Exercise 6: Create and upload concepts with varied data-types
   1. Files concept.csv fact.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