informatics for integrating biology and the bedside

Introduction to i2b2Informatics for Integrating Biology and the Bedside

i2b2 Introductory Training V2.9

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.

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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Research tool continuum

Hypothesis

Collaboration

Data capture

Analysis

Publication

i2b2 Cohort Discovery Tool

Research Networking

Electronic Data Capture

Statistics

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What is the source of the data?

Health Factsmulti-million

patient database

EMR and billing data from 100+ other

organizations

PSH EMRdata

PSH Billingdata

Penn State i2b2

(January 2011 onward)

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What does the data contain?De-identified data for over 585,000 unique patientsBasic demographics (age, sex, race, ethnicity)ICD-9 diagnoses and ICD-9 procedures coded for

HMC billingLab tests performed by HMC(Inpatient) medications administered by HMCVisit types (inpatient, outpatient, emergency, same

day care, etc.)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 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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Setting expectations… i2b2 is a vast collection of data, but it does not contain all

data types that you might need. Not included are: 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 infusions4/2/14


Setting expectations… Not included currently, but potential enhancements are:

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

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From hypothesis to data collection

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Develop criteria for queries and refine to establish the cohort

Re-query and request a Patient Set Review aggregate data and refine

IRB approvalRequest standard data set from Decision Support based on query

Export data for preliminary exploration and analysis – OR – Request a de-identified data set from Decision Support based on query


A quick cohort example Patients with the diagnosis of alcohol withdrawal

Find the ICD code for alcohol withdrawal usingFind Terms, Search by Names

Query for all patients with ICD diagnosis of 291.81

~412 patients

Date restrict the search to 1/1/2013 to 03/01/2013

~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 ~17 patients

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Refining i2b2 queriesi2b2 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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Now that I have enough patients in the cohort, what is next?Rerun the same query requesting patient set, by checking Patient ListUse 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 dataRequest data set from Decision Support

Turnaround time will be approximately 3 daysThe dataset you receive will be a standard data set, either de-

identified or with HIPAA identifiers depending on what you have rights to see (IRB-determined or TPO)

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i2b2 Analysis ToolsDemographics

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 data exportFrom the Specify Data tab:

1. At the bottom pane of the screen, under Plugins, select ExportXLS2. Drag the Alcohol Withdrawal patient set into the Patient Set box3. Navigate the Ontology pane to locate Benzodiazepines, then drag this parent

folder to the Concept(s) box4. Navigate the Ontology pane to locate Electrolytes – single valence, then drag

this parent folder to the Concept(s) box5. 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.4/2/14


Important caveat about coded termsThe i2b2 Ontology lists >450,000 individual terms, but only a small

subset of these terms are populated in Penn State’s i2b2. 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.

If you choose a term with zero patients, then your i2b2 query will return no patients for that query.

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i2b2 query assistancei2b2’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: 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.

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 path4/2/14


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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SupportTraining, patience, and experience are the keys

Need assistance?We can provide individual help. Contact i2b2 Support at

[email protected] in on i2b2/REDCap Open Office Hours every Thursday,

3:30 pm – 4:30 in Room H4510J.Consult your i2b2 Guidebook and FAQ documentUse the i2b2 query assistance spreadsheet that lists the codes

populated in our i2b2Visit the i2b2 website at http://ctsi.psu.edu/?page_id=3690

4/2/14 i2b2 Introductory Training V2.9

https://mail.hmc.psu.edu/owa/redir.aspx?C=3wWWKE5ejECBIwRqDE-Q19gei437cdAIxnQ__oUqQYEpBAZ0xEfPyIj-lOHFzDVLfyts_1so_gY.&URL=mailto:[email protected]

http://ctsi.psu.edu/?page_id=3690

informatics for integrating biology and the bedside

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