CIDER - Today’s research, Tomorrow’s treatments Lab-2 September 15, 2010 Bijoy George, Program Manager, CBMI

CIDER - Today’s research, Tomorrow’s treatments

Lab-2September 15, 2010

Bijoy George, Program Manager, CBMI

http://cbmi.wustl.edu/

Summary from Last Class

Introduction to CIDER Opt Out Security and Auditing User responsibilities Definition of Project Data privileges Process workflows – user activation & project

creation Session Timeout

Quiz Results

1

2

3

4

5

6

7

8

9

10

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

CIDER Quiz-1 Results from 9/8/2010

Correct Answer

Review Quiz

Q-1 What trainings are mandatory for a user to activate

his/her user account in CIDER?

Q-4 As a Washington University user, what should you do

in the event of you losing OR compromising the downloaded data from CIDER?

Q-8 A user can query and view clinical data without using

a project. - True/ False

Agenda for Today

Introduction to Menus Introduction to Dashboard Introduction to Vocabulary Interface Types of Queries in CIDER Use of shared and parameterized query CIDER Application demo Hands on Lab Quiz Q&A

Dashboard

Dashboard is the page on which users would be taken to upon successful login

All items available to user are organized on this page under the Explorer

Can filter/search for a particular item Can customize number of records per page Pagination enabled at the top

Dashboard

Dashboard

Vocabulary Interface

BJC uses a custom coding system based on SNOMED 1993

It is called MED – Medical Entities Dictionary Vocabulary Interface establishes the mapping

b/w standard vocabularies Permissible values can be searched and

selected while forming queries The lab unit of measure, lab specimen type and

number of occurrences next to the codes

Vocabulary Interface

Vocabulary Interface

Vocabulary Interface Demo

Provides Permissible Values (PVs) for clinical variables in Demographics Visits Lab Tests Medications Documents

Demographics

Gender Ethnic Origin Race       

Visits

Patient Type Discharge Service Admitting Service Facility Procedure Code Diagnosis Code

Lab Tests

Specimen Type Laboratory Procedure Type Facility Laboratory Test Type

Medications

Medication Medication Order Route Medication Component Route Medication Component Type Frequency

Documents

Document – can do ‘google like’ search Document Name (Type) Facility  

Introduction to Queries

Two types Discover patient cohorts Obtain patient data

How to use Shared Queries

Shared and Parameterized Queries Introduction

Selecting permissible values Adding permissible values Run query interactively or in background History available under Recent Queries

Application Demo

Find patients with a particular Diagnosis Find patients with a particular Procedure Find patients having a Lab Test done Find patients who had taken a particular

Medication

Hands on Lab-2

Use queries from Shared Queries to find out the

following for an unspecified project:

1. Find the number of patients with Type-2 Diabetes

2. Find the number of patients with Hypertrophic Cardiomyopathy (HCM)

3. Find number of patients with elevated levels of Troponin ( level > 0.2 nanograms per milliliter )

Quiz-2

Please write your First name and Last Name on the quiz answer sheet to get proper credit

Please circle the best answer choice for each question

Please turn in the completed assignments to me before the end of the class

We will go over the answers and you will get your answer papers graded in the next class

Take Home Assignment

Identify whether there are enough patients to conduct a study for your project and report the results by next class

OR

Find the number of patients over the age 40 with breast cancer diagnosed. Breast Cancer ICD-9 codes are as follows. [ICD-9 = 174 ->174.9 and

ICD-9 = 233.0)AND

Review CIDER help pages for Lab-3 Working with Workflows

http://wikip2m1.cbmi.wucon.wustl.edu/ciderwiki/

Appendix

CIDER Screen shots

Menu Options

My DashboardMy Profile

Menu OptionsSearch

New Search- Get Count

- Workflow

Menu Options My ProjectsMy Queries

My WorkflowsApprove User

Request

Dashboard

Components of Dashboard Projects

Projects

My Projects

View Project

View Project

Back to Project List

Dashboard

Introduction to Dashboard Projects Queries

• Recent Queries• My Queries• Shared Queries

Recent Queries

Run statusCompleted

Failed

Counts

View Parameters

View Parameters under Recent Queries

Query Parameters

My Queries

# of Queries

Query Type

Edit Query

Execute Query

Query Title

Shared Queries

Edit Query

Execute Query

Dashboard

Introduction to Dashboard Projects Queries Workflows

Workflows

Workflows

Dashboard

Introduction to Dashboard Projects Queries Workflow Message Board

Q & A

Please feel free to contact me at any time Email: [email protected]