Informatics for Integrating Biology and the Bedside
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 Introductory Training V2.9
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.
 For example, an i2b2 query specifying a lab test will return the
number of patients who had that test during the specified
time, but not how many times that test was performed for
each patient, or the results for each test performed.
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i2b2 Introductory Training V2.9
Research tool continuum
Electronic Data
Capture
i2b2 Cohort
Discovery Tool
Hypothesis
Data capture
Collaboration
Research
Networking
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i2b2 Introductory Training V2.9
Publication
Analysis
Statistics
What is the source of the data?
EMR and billing data
from 100+ other
organizations
PSH EMR
data
Health Facts
multi-million
patient database
Penn State i2b2
(January 2011 onward)
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i2b2 Introductory Training V2.9
PSH Billing
data
What does the data contain?
 De-identified data for over 585,000 unique patients
 Basic demographics (age, sex, race, ethnicity)
 ICD-9 diagnoses and ICD-9 procedures coded for HMC
billing
 Lab tests performed by HMC
 (Inpatient) medications administered by HMC
 Visit types (inpatient, outpatient, emergency, same
day care, etc.)
 Key dates associated with each event above
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i2b2 Introductory Training V2.9
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
 i2b2 User Guide and FAQ
 i2b2 lookup guide for procedures, diagnoses, meds and lab tests
 Sample i2b2 queries and their results
 Listing of the Standard Data Set
These materials can be found in the i2b2 website (www.ctsi.psu.edu/?=page_id=3706).
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i2b2 Introductory Training V2.9
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
Outpatient medications and continuous infusions
i2b2 Introductory Training V2.9
Setting expectations…
 Not included currently, but potential enhancements are:
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Most outpatient procedures (CPT)
Additional demographics (date of birth (shifted))
Tissue availability in our bio-repository, or consent to be
contacted for research
Cancer Registry
i2b2 Introductory Training V2.9
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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i2b2 Introductory Training V2.9
A quick cohort example
Patients with the diagnosis of alcohol withdrawal
 Find the ICD code for alcohol withdrawal using
Find Terms, Search by Names
 Query for all patients with ICD diagnosis of 291.81
 Date restrict the search to 1/1/2013 to 03/01/2013
~412 patients
~20 patients
 Navigate the ontology to find Benzodiazepines
 Drag Benzodiazepines (parent folder) to Group 2 query
~19 patients
 Apply a temporal constraint of same financial
encounter for both the Dx and Benzodiazepines
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i2b2 Introductory Training V2.9
~17 patients
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.
 Similarly, i2b2 can restrict lab result queries to values falling
within a certain range (e.g., > 100 mg/dL).
In all cases, however, i2b2 counts reflect unique patients.
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i2b2 Introductory Training V2.9
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 3 days
 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 TPO)
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i2b2 Introductory Training V2.9
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 encounter, Alcohol Withdrawal 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 Introductory Training V2.9
i2b2 data export
From the Specify Data tab:
1. At the bottom pane of the screen, under Plugins, select ExportXLS
2. Drag the Alcohol Withdrawal patient set into the Patient Set box
3. Navigate the Ontology pane to locate Benzodiazepines, then drag this parent
folder to the Concept(s) box
4. Navigate the Ontology pane to locate Electrolytes – single valence, 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, Vital Status)
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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i2b2 Introductory Training V2.9
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.
i2b2 Introductory Training V2.9
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
 From the Penn State CTSI i2b2 Web site, you can request a query
assistance spreadsheet to ease the process, especially for meds
and labs.
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Use Excel’s Find function to locate the term that you seek
Use the resulting code(s) in i2b2’s Find Terms, Search by Codes
or use Navigate Terms and follow the listed i2b2 Ontology path
i2b2 Introductory Training V2.9
Requesting Standard Data Set
 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 to
clipboard.
 Submit a Report Request to IT:
 Infonet > Departments > Technical/IT > Our Services > Request Report
 Complete the form as follows:
 Source: Connected EMR
 Detail: Identify this as an i2b2 query and including the query name (paste from
clipboard)
 If you are requesting PHI for research, include the IRB number.
 Other dates: not used
 The report (spreadsheet) will appear in your Infoview inbox:
 Internet browser > URL = myapps > login > folders (Business Objects) > Infoview
 Please note that the standard data set may be large. You might consider providing
IT with a date range. PHS can also assist with the data reduction.
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i2b2 Introductory Training V2.9
Support
 Training, patience, and experience are the keys
 Need assistance?
 We can provide individual help. Contact i2b2 Support at
i2b2@hmc.psu.edu
 Drop in on i2b2/REDCap Open Office Hours every Thursday,
3:30 pm – 4:30 in Room H4510J.
 Consult your i2b2 Guidebook and FAQ document
 Use the i2b2 query assistance spreadsheet that lists the codes
populated in our i2b2
 Visit the i2b2 website at http://ctsi.psu.edu/?page_id=3690
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i2b2 Introductory Training V2.9