Summary from Last Class

2. 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

3. Quiz Results

4. 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

5. 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

6. 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

7. 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.

8. 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.

9. View Results • Tree view • Spreadsheet view

10. 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

11. 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

12. 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)

13. 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.

14. 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

15. Q & A • Please feel free to contact me at any time • Email: bgeorge@wustl.edu

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

17. Steps to create a query

18. Develop query • Metadata • Attributes • Permissible values • Adding limits • Diagrammatic view

19. 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.

20. How to form a temporal query Step-2: Click to add Temporal condition Step-1: Click on one or two objects to highlight

21. Add Temporal condition Name the temporal result field Time Interval

22. Temporal condition displayed on DAG Temporal condition

23. Edit/Delete Temporal condition Edit / Delete