1. CIDER - Today’s research, Tomorrow’s treatments Lab-2 September 15, 2010 Bijoy George, Program Manager, CBMI http://cbmi.wustl.edu/

2. 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

3. Quiz Results

4. 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

5. 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

6. 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

7. Dashboard

8. 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

9. Vocabulary Interface

10. Vocabulary Interface Demo  Provides Permissible Values (PVs) for clinical variables in  Demographics  Visits  Lab Tests  Medications  Documents

11. Demographics  Gender  Ethnic Origin  Race

12. Visits  Patient Type  Discharge Service  Admitting Service  Facility  Procedure Code  Diagnosis Code

13. Lab Tests  Specimen Type  Laboratory Procedure Type  Facility  Laboratory Test Type

14. Medications  Medication  Medication Order Route  Medication Component Route  Medication Component Type  Frequency

15. Documents  Document – can do ‘google like’ search  Document Name (Type)  Facility

16. Introduction to Queries  Two types  Discover patient cohorts  Obtain patient data

17. 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

18. 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

19. 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 )

20. 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

21. 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/

22. Appendix CIDER Screen shots

23. Menu Options My Dashboard My Profile

24. Menu Options Search New Search - Get Count - Workflow

25. Menu Options My Projects My Queries My Workflows Approve User Request

26. Dashboard  Components of Dashboard  Projects

27. Projects My Projects View Project

28. Back to Project List

29. Dashboard  Introduction to Dashboard  Projects  Queries Recent Queries My Queries Shared Queries

30. Recent Queries Run status Completed Failed Counts View Parameters

31. View Parameters under Recent Queries Query Parameters

32. My Queries # of Queries Query Type Edit Query Execute Query Query Title

33. Shared Queries Edit Query Execute Query

34. Dashboard  Introduction to Dashboard  Projects  Queries  Workflows

35. Workflows

36. Dashboard  Introduction to Dashboard  Projects  Queries  Workflow  Message Board

37. Q & A  Please feel free to contact me at any time  Email: bgeorge@wustl.edubgeorge@wustl.edu