CIDER - Today’s research, Tomorrow’s treatments Lab-3 September 22, 2010 Bijoy George, Program Manager, CBMI

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

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 

Appendix  Intro to developing queries to discover patient cohorts using Simple method  Categories  Diagrammatic (DAG) View ( DAG definition ) 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