Transcript i2b2 Introductory Training

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
What is the source of the data?
Cerner
Millennium
Updated daily
Eclipsys & Signature
Billing Systems
Cancer
Registry
Updated daily
Updated monthly
Operational
Data Store
Data goes through de-identification process
i2b2 - PSU
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Personalized
Medicine
Updated monthly
What does the data contain?
 De-identified data for over 730,000 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
Diagnoses and procedures (inpatient) coded with ICD-10 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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Uses Cases, Strengths & Limitations
 Intended uses
 Cohort identification for research
 NOT intended for clinical workflow
 Strengths and limitations
 Quick turnaround for count of patients
 Immediate export capability of many concepts (de-identified)
 Visualization tools for looking at demographic data in
aggregate and timeline of events
 Useful for retrospective studies using source data for
secondary use.
 No imaging or narrative data
 Works best when you know the underlying codes
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What i2b2 does NOT contain…
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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
Coming soon…..
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Problem Lists
Height, weight, BMI, Systolic and Diastolic BP, Temperature, Heart Rate
Attending physician & NPI #
Department location
Smoking Assessments
ICD-o for Oncology
Pulmonary Function Tests
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From hypothesis to data collection
Develop queries and refine for cohort
Use Analysis Tools to review data then refine the query as needed
Export data for preliminary exploration and analysis – OR – Request a
Standard Data Set or custom data set from Decision Support based on
query
• Without IRB approval – de-identifed data set
• With IRB approval – data set with identifiers
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I2b2 Tool Panel
The left panel will be available for both the Find Patients and
Analysis Tools using i2b2
 Concept Group
 Lists all data concepts
found within i2b2
 Workplace
 Favorites/Bookmarked
concepts/queries
 Previous Queries
 All of your prior queries
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I2b2 Tool Panel (continued)
 Query Tool
 Groups to gather your concepts for searching
(ANDs and ORs)
 Results and Graphs
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i2b2 Searching for Terms
i2b2’s Navigate Terms and Find Terms functions allow you to select
your query terms.
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Resources for code lookups
 Use Google to search for the following codes:
 ICD-9
 ICD-10
 CPT
 LOINC
 RxNorm
Or use the below websites that provide lookup tables:
 ICD-9: https://www.cms.gov/medicare-coverage-database/staticpages/icd-9-
code-lookup.aspx
 ICD-10: https://www.cms.gov/medicare-coverage-database/staticpages/icd10-code-lookup.aspx
 LOINC: https://search.loinc.org/
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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
~5320 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
Additional Query Refinement
i2b2 provides different ways to refine your queries. For example:
 Temporal Constraint: constrains the timing of observed
concepts for ALL groups.
 Date constraints: constrains dates for all terms within the
group.
 # of occurrences (i.e., occurs > 4 times): only patients
returned would be those who had 5 or more occurrences in
that time period within the group.
 Exclude: will exclude all patients who have
observations/demographics within the group.
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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 de-identified data
 Timeline and Export tools will allow for additional data, not considered as
part of the filter criteria. All data is available for that cohort.
 Request data set from Decision Support
 Turnaround time will be 5-7 business days for the Standard Data Set.
 The dataset you receive will be a standard data set, either de-identified or
with HIPAA identifiers depending on what you have rights to see (IRBdetermined or non-research)
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i2b2 Analysis Tools Example
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 Example
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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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 > Request a Report (bottom of page)
 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. If you wish to have a subset
of the standard data set, then indicate the items and Decision Support will remove the unwanted data.
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:
 Myapps (found in the Start menu) > 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
 Contact all 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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i2b2 Introductory Training V3.10