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

Before session:

Agenda

Welcome and introduction: Kavi (10 minutes)

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

20,000 feet view: 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