Additional Tutorials and Documentation
Space shortcuts
Space Tools
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 9 Next »

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

Agenda

Start_timeSessionMinutes
1:00 PMAudience intro + env : Kavi Wagholikar20
1:20 PMShawn Murphy: 20000 foot view20
1:40 PMJeff Klann: Query Tool and networks20
2:00 PMTeam formation 15
2:15 PMBREAK15
2:30 PMMike Mendis: i2b2 on OMOP database20
2:50 PMKavi Wagholikar: Loading Data20
3:10 PMTeam discussions40
3:50 PMWrap up40
4:30 PMEnd-


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


  • No labels