CIDER - Today’s research, Tomorrow’s treatments

Lab-3September 22, 2010

Bijoy George, Program Manager, CBMI

http://cbmi.wustl.edu/

Summary from Last Class

Introduction to Menus Introduction to Dashboard Introduction to Vocabulary Interface Types of Queries in CIDER Use of shared and parameterized query

Quiz Results

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CIDER Quiz-2 Results

Correct Answer

Review Quiz

Q-2: If you would like to see the results (patient counts) of a query you have recently executed, which one of the following folders on the Dashboard under Explorer will give you that information?

Q-3: In CIDER, clinical data is stored in the repository using which one of the Vocabulary

systems?

Q-4: You have used a shared and parameterized query to identify the number of patients diagnosed with Acute Coronary Syndrome (ACS). You realize that you do not need one of the conditions (Gender = Male only) specified in the shared query for your study because your study includes both males and females. During execution time, can you remove this condition?

Q-5: the Vocabulary Interface, the number next to the permissible value codes for Diagnosis,

Procedures, Lab etc. is the number of occurrences of that code in CIDER. –True / False

Q-7: You always need a project to run queries to identify patient cohorts. -- True / False

Q-8: If you already have a study approved, it is best practice that you should create the project before trying to execute queries and use that project to discover patient cohorts. – True/ False

Q-10: If you are an investigator in CIDER, the notification that your data download request is complete will appear under your Message Board in CIDER – True/ False

Agenda for Today

Introduction to Query Workflow Use of shared queries in a Workflow Set Operations / Other Functions View results

Tree view Spreadsheet view

Exporting de-identified data out of CIDER CIDER Application demo Hands on Lab Quiz Intro to developing queries to discover patient cohorts

using Simple method

Query Workflow

A Workflow is a collection or a group of queries that can be executed either individually or collectively, to obtain or view results for a specific research.

In other words, a workflow is a container that contains a set of queries.

Workflow can include two types of queries Discover patient cohorts Obtain Patient Data

Query Workflow

Organization of queries Can form set operations to discover patient cohorts

Union Intersection Minus (left outer join)

Data queries can only be created & executed in a workflow

A user can create as many workflows and also can add as many queries in a workflow, as needed.

Obtain Patient Data

Execute the data query by clicking on Execute after selecting patient cohort query from the drop down

The parameter list will be displayed to confirm the values

Once executed, the Results will be displayed with a Tree view on left and a Spreadsheet view on right

To minimize the wait time, the application displays the page as soon as few patient’s data is assembled.

View Results

Tree view Spreadsheet view

Export Data

After reviewing the data online, click on Export link to export de-identified data

User has to agree to the terms and conditions for data download to continue

The data will be exported in an Excel workbook De-Identified data can be downloaded to a

user’s PC

Application demo

How to create a workflow How to add discover patient cohort queries to a

workflow How to do ‘google like’ search on reports How to use set operations and how can it help

to discover the patient cohorts How to add patient data queries to a workflow View results – Tree/spreadsheet view Export data

Hands on Lab

Create a new workflow for Diabetes and ACS study (Use the Project you have created)

Add 2 more patient cohort discovery queries, similar to the one created in Lab-2 as follows Find all ACS patients (Acute Coronary Syndrome) (a)

• Include patients with Acute Myocardial Infarction• ICD9 codes 410 and 412

Find all patients who are diagnosed for Diabetes (b)

Form operations on the above queries to find out How many patients have both ACS & Diabetes (a

intersection b) How many ACS patients with no Diabetes (a minus b)

Hands on Lab

Use a parameterized and shared data query to get the following clinical data of patients and add it to the workflow. Age Gender Race Troponin level Collection timestamp

Use the data query to obtain patient data.

Quiz-3

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

Q & A

Please feel free to contact me at any time Email: bgeorge@wustl.edu

Appendix

Intro to developing queries to discover patient cohorts using Simple method

Categories Diagrammatic (DAG) View (DAG definition)

Steps to create a query

Develop query

Metadata Attributes Permissible values Adding limits Diagrammatic view

Temporal Queries

Queries with temporal conditions Researchers often need to obtain patient information and

other information on time and quantity. For example, a specific type of test done after a certain age

limit, or total medication given to a patient at a particular age Querying such calculated information is not possible using a

normal query Temporal query uses the Time and Quantity attribute to

enable time-based operations to return calculated results. The time-based attributes are date, age, and so on. The quantitative attributes are Age at Procedure from the

Laboratory Procedure Details class, and so on.

How to form a temporal query

Step-2: Click to add

Temporal condition

Step-1: Click on one or

two objects to highlight

Add Temporal condition

Name the temporal

result field Time Interval

Temporal condition displayed on DAG

Temporal condition

Edit/Delete Temporal condition

Edit / Delete