Informatics for Integrating Biology and the Bedside
Presented by:
Terri Shkuda
i2b2 Administrator
Research Informatics
Efforts are supported by: Clinical and Translational Science Award
Grant # UL1TR000127
What is i2b2?
i2b2 = informatics for
integrating
biology and the
bedside
 Developed at Harvard Partners Healthcare through a
CTSA grant.
 Simple user interface to query selected clinical and
billing data from Penn State Hershey care delivery from
January 2011 to present.
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i2b2’s fundamental purpose
Cohort identification - Users search a de-identified database,
without IRB approval, to determine the existence of a set of
patients meeting specified criteria.
The data are presented as unique patient counts. This means a
patient is counted exactly once if he/she ever met the criteria
specified by the query.
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Research tool continuum
Electronic Data
Capture
i2b2 Cohort
Discovery Tool
Hypothesis
Data capture
Collaboration
Research
Networking
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Publication
Analysis
Statistics
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What is the source of the data?
Cerner
Millennium
Eclipsys & Signature
Billing Systems
Cancer
Registry
Personalized
Medicine
Operational
Data Store
i2b2 - PSU
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What does the data contain?
 De-identified data for over 665,000 unique patients
 Basic demographics (age, ethnicity, gender, language, marital status, race,
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religion, vital status)
Diagnoses and procedures (inpatient) coded with ICD-9 for HMC billing
Procedures coded with CPT (outpatient)
Lab tests performed by HMC
Medications (administered during inpatient, med list reported at
outpatient)
Personalized Medicine (sample availability, consent for research, tobacco)
Visit types (inpatient, outpatient, emergency, same day care, etc.)
Cancer Registry
Key dates associated with each event above
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What will we accomplish today?
 You’ll receive an overview of i2b2, including:
 Intended uses
 Strengths and limitations
 You’ll see a few i2b2 queries, supplemented by materials to
facilitate your subsequent hands-on learning.
 This PowerPoint presentation
 Listing of the Standard Data Set
These materials can be found in the i2b2 website (http://ctsi.psu.edu/ctsi-programs/clinicalservices-core/training-resources/).
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Setting expectations…
 i2b2 is a vast collection of data, but it does not contain all
data types that you might need. Not included are:
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Summaries and clinic notes (free-form text)
Narrative reports (e.g., radiology, surgical pathology, operative
reports)
Images (e.g., digital x-rays, EKGs, scanned documents)
Microbiology data (not yet recorded discreetly in the EMR)
Family History and Medical History (unless coded for billing purposes)
Genomic data
Problem Lists
Height, weight, vital signs, allergies, and other data from nursing
forms
Primary/Attending physician
Department location
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From hypothesis to data collection
Develop criteria for queries and refine to establish the cohort
Re-query and request a Patient Set
Review aggregate data and refine
Export data for preliminary exploration and analysis – OR –
Request a de-identified data set from Decision Support based on
query
IRB approval
Request standard data set from Decision Support based on query
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A quick cohort example
Patients with the diagnosis of Strep Throat and Scarlet Fever:
 Find the ICD diagnosis for Streptococcal Sore Throat and Scarlet Fever using
Find Terms, Search by Names
 Query for all patients with the ICD diagnosis
 Date restrict the search to 1/1/2013 to 03/01/2013
~4884 patients
~260 patients
 Find the CPT for Strep test searching for the “CPT rapid strep test” on
Google, then search using Find Terms, Search by Codes, CPT (87880)
 Drag the Rapid Strep CPT code (87880) to Group 2 query
~35 patients
 Apply a temporal constraint of same financial
encounter for both the Dx and Procedure
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~30 patients
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i2b2 query assistance
i2b2’s Navigate Terms and Find Terms functions allow you to select
your query terms. The tips below might help you.
 Sometimes, it’s easier to:
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Perform an Internet search on the concept + the coding system:
for example: heart failure ICD code
Use the resulting code(s) in i2b2’s Find Terms, Search by Codes
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Refining i2b2 queries
i2b2 provides different ways to refine your queries. For example:
 You can specify whether the concept ever occurs or occurs at
least a certain number of times in a defined time period.
 If you specified occurs > 4 times, then the only patients counted
would those who had 5 or more occurrences in that time period.
In all cases, however, i2b2 counts reflect unique patients.
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Now that I have enough patients in the
cohort, what is next?
 Rerun the same query requesting patient set, by checking Patient List
 Use visualization tools:
 Demographic composition shows the distribution of age, sex, race,
and vital status
 Timeline plug-in depicting temporal relationships among its
“concepts” (diagnoses, meds, lab tests) timing of their occurrence.
 Export data
 Request data set from Decision Support
 Turnaround time will be approximately 5-7 business days for the
Standard Data Set.
 The dataset you receive will be a standard data set, either deidentified or with HIPAA identifiers depending on what you have
rights to see (IRB-determined or non-research)
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i2b2 Analysis Tools
Demographics
 Switch from Find Patients to Analysis Tools (make this
selection at the very top right section of the Web page)
 From the Plugins tab at the bottom:
 Select the plug-in called Demographics (1 Patient Set)
 For Patient Set, use the last query, Strep with Scarlet Fever patient
set and choose the Patient Set in the Previous Queries tab.
 Drag the Patient Set to the Patient Set field in the Analysis Tool
window.
 Select the View Results tab
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i2b2 data export
From the Specify Data tab:
1. At the bottom pane of the screen, under Plugins, select ExportXLS
2. Drag the Strep with Scarlet Fever patient set into the Patient Set box
3. Locate Strep Test in your Workplace, then drag this to the Concept(s) box
4. Navigate the Ontology (Medications) pane to locate Amoxicillin, then drag this
parent folder to the Concept(s) box
5. Under Output Options:
• For Formatting, select 1 row per observation (detailed, 1 column per obs…)
• For Demographic data, select a few (e.g., Sex, Age)
6. Under Options (may cause long running time):
• Select Resolve Concept/Modifier Codes
Select the View Results tab, then wait until the export is displayed.
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Important caveat about coded terms
 The i2b2 Ontology lists >450,000 individual terms, but only a small
subset of these terms are populated in Penn State’s i2b2.
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For example, hundreds of acetaminophen products are sold in the
U.S. Fewer than 20 are part of HMC’s drug formulary and thus
populated in Penn State’s i2b2.
 Since not all available i2b2 terms are populated with HMC data,
you must construct your queries carefully. At the far right of
several terms in the Ontology pane (diagnoses, procedures,
medications, lab tests), you can see which terms are populated.
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If you choose a term with zero patients, then your i2b2 query will
return no patients for that query.
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Requesting Standard Data Set
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Once you are satisfied with your patient set, you may request a Standard Data Set from Decision Support
which will encompass all dates for the patient.
Locate your query in the Previous Queries or Workplace window and copy the entire name to clipboard.
Submit a Report Request to IT:
 Infonet > Support Services (bottom of main page) > Information Technology > Request a Report
 Click on Report and Service Request Form
 Log into BMC Remedy with your EPASS, select the Request Now button and complete the form as follows:
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Type of Request: New Report
Source: Connected EMR
Provide a detailed description of your request including data fields: Identify this as an i2b2 query and
including the query name (paste from clipboard), requesting a standard data set.
Date Report Needed: for Standard Data Set, allow for at least 5-7 business days, for custom report, allow for
4 weeks.
Reason for Request: Research
Research Request Type: Choose the appropriate funding selection
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Complete the remaining subfields with type of research and IRB # (if requesting PHI).
The report (spreadsheets) will appear in your LaunchPad inbox and a representative from Decision Support will
contact you:
 Internet browser > URL = myapps > login > folders (Business Objects) > LaunchPad > Documents > Inbox
Please note that the standard data set may be large. PHS can also assist with the data reduction.
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Support
 Training, patience, and experience are the keys
 Need assistance?
 We can provide individual help. Contact call the Help Desk
at 717-531-6281 requesting help with i2b2-PSU. A ticket
will be sent to i2b2 Support.
 Drop in on i2b2/REDCap Open Office Hours every Thursday,
3:00 pm – 4:00 in HMC, Room H4510J.
 Visit the i2b2 website at http://ctsi.psu.edu/ctsiprograms/clinical-services-core/i2b2-home
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