Download - Summary from Last Class
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CIDER - Today’s research, Tomorrow’s treatments
Lab-3September 22, 2010
Bijoy George, Program Manager, CBMI
http://cbmi.wustl.edu/
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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
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Quiz Results
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CIDER Quiz-2 Results
Correct Answer
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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
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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
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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
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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.
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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.
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View Results
Tree view Spreadsheet view
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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
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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
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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)
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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.
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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
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Appendix
Intro to developing queries to discover patient cohorts using Simple method
Categories Diagrammatic (DAG) View (DAG definition)
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Steps to create a query
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Develop query
Metadata Attributes Permissible values Adding limits Diagrammatic view
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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.
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How to form a temporal query
Step-2: Click to add
Temporal condition
Step-1: Click on one or
two objects to highlight
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Add Temporal condition
Name the temporal
result field Time Interval
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Temporal condition displayed on DAG
Temporal condition
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Edit/Delete Temporal condition
Edit / Delete