i2b2: Training Manual

2015

INTRODUCTION TO USING DE-IDENTIFIED WAREHOUSE JEREMY NIX

CINCINNATI CHILDREN'S HOSPITAL MEDICAL CENTER | Biomedical Informatics - Data Services

i2b2 Training Manual 1

Contents i2b2 Background and Overview ................................................................................................................................................................. 2

Data Specifics ............................................................................................................................................................................................. 3

Logging in ................................................................................................................................................................................................... 4

Workbench Overview ................................................................................................................................................................................ 5

Ontology ................................................................................................................................................................................................ 5

Folder Navigation ............................................................................................................................................................................... 5

Ontology Search ................................................................................................................................................................................. 6

Query Tool ............................................................................................................................................................................................. 6

Query-Specific Options: ..................................................................................................................................................................... 7

Group-Specific Options: ..................................................................................................................................................................... 7

Concept-Specific Options: .................................................................................................................................................................. 7

Previous Queries .................................................................................................................................................................................... 7

Workplace .............................................................................................................................................................................................. 8

Getting Started Guide ............................................................................................................................................................................ 8

Query Verbalizer .................................................................................................................................................................................... 9

Creating a Simply Query ............................................................................................................................................................................ 9

Advanced Query....................................................................................................................................................................................... 12

Summary .................................................................................................................................................................................................. 13

i2b2 Training Manual 2 i2b2 Background and Overview i2b2 (Informatics for Integrating Biology and the Bedside) is an NIH-funded National Center for Biomedical Computing based at

Partners HealthCare System. i2b2 was developed as a scalable informatics framework designed for translational research. i2b2 was

designed primarily for cohort identification, allowing users to perform an enterprise-wide search on a de-identified repository of

health information to determine the existence of a set of patients meeting certain inclusion or exclusion criteria.

In lamens terms, i2b2 allows researchers to determine feasibility of a Study by identifying whether or not a sizable amount of

patients exist with their Study-specific criteria

i2b2 Training Manual 3 Data Specifics The CCHMC institutional i2b2 data warehouse is under constant evolution. Whether it be sheer amounts of data (patients / visits),

types of data (labs / meds) or organization of data (ICD10 / SNOMED), there is a constant flow of change meant to improve upon the

types of research related questions that can be solved. Below is the current domains of data that can be found within i2b2:

Allergy Data

Biobank Sample Data

Demographic Data

Diagnosis Data

Flowsheet Data

Laboratory Data

Medication Data

Procedure Data

Social History Data

Visit Detail Data

The list of de-identified data domains will only grow with time.

i2b2 Training Manual 4 Logging in To access i2b2, navigate to: https://i2b2.research.cchmc.org/i2b2web/

Fill in your CCHMC username and password and click on the Submit button. If you experience troubles while logging in, please

contact help-i2b2@bmi.cchmc.org.

After you log in, you will be brought to the i2b2 Workbench (below). Note your user name, link to Logout, and a link to provide

Feedback to the i2b2 team in the upper right hand corner of your screen:

i2b2 Training Manual 5 Workbench Overview Before we create a new query, let’s take a moment to review the Workbench layout:

Ontology This section is where you will browse for concepts (criteria) to include in your query. The ontology is simply a hierarchial

representation of terms. The tree structure starts out being less specific. As you navigate through the ontology tree,

terms/categories become more and more specific.

Folder Navigation The Ontology is represented as a tree folder structure, not unlike what

your Windows Explorer might display as you navigate files/folders on your

computer.

Expand (Open) a Folder

1. Click on the sign next to the folder in the Navigate Terms View.

2. The folder will open and all the items in the folder will display.

Collapse (Close) a Folder

1. Click on the sign next to the folder in the Navigate Terms View.

2. The folder will close and all the items in the folder will no longer

appear in the view.

i2b2 Training Manual 6 Ontology Search Navigating the Ontology can be time consuming and difficult, especially if you are unsure as to how a particular concept or term has

been organized. To make things easier, we have provided a search feature in the Ontology section. by typing in your criteria and

clicking the search icon, the ontology tree is replaced with a list of search results.

To include all of the matching terms in your search criteria, click on the Select All button and drag the terms into the desired query

panel.

To get back to the initial ontology view, click on the Reset link.

Query Tool Concepts can be added to the query tool by dragging the concept from the Navigate/Find Terms section to the "Drag terms here"

box at the bottom of each group within the Query Tool.

i2b2 Training Manual 7 Query-Specific Options:

New Query: Remove the content of all groups (the entire query)

Add Group: Three groups appear by default; you can add additional groups by clicking "Add Group"

Save Query Definition: Saves your query criteria into your personal Workplace for later use (common query).

Run Query: Click "Run Query" when you have entered all of your concepts

Group-Specific Options:

Group specific options can be found by clicking on the Menu Icon in the top left corner of the group panel

Limit By Date: Specify a date range for which the criteria within this Group should be applied to.

Limit By ID: Newer feature used to limit your results to a specific set of patients based on identifiers like MRN or PAT_ID.

Limit By Occurrence: Match patients where the Group's criteria occurs at least X # of times, or less than X # of times, etc.

Toggle Include/Exclude: Choose to match patients where the Group's criteria matches (include) or to match patients where

the Group's criteria doesn't match (exclude)

Age at Event (all terms): Look for patients where the concepts listed in the Group all occur based on the age restrictions

specified.

Reset Group: Clears all query customations for the Group and resets it back to the initial state.

Concept-Specific Options: Concept specific options can be found by right clicking on a concept / term.

Remove: Removes the term from the Group.

Age At Event: Looks for patients where the concept / term / criteria occurred when the patient's age matched the criteria.

Constrain By Value: Some concepts may have text or numeric values attributed to them. You can use this filter dialog to

further constrain your criteria.

Constrain By XML (Filter By Attribute): Advanced filtering option that is enabled on some categories of concepts. Upon

clicking, you will be given the ability to further filter/constrain by additional attributes of the concept. Examples:

o Medications: Filter by active medication vs inactive medication

o Diagnosis: Filter by Encounter diagnosis, or Billing diagnosis

Previous Queries Previously run queries will save to this section and will group by date the query was run. Expanding the date folder will display any

queries that were executed on that date. Expanding on a query will display results produced by the query. In the below example,

the query for birth year of 1993 returned 33,442 patients. Hovering over the query folder and result items will display additional

details about the results (time to run, status, etc.).

i2b2 Training Manual 8 Right clicking on a query folder.

Apply Query Criteria: Replaces all of the current query criteria in the Query Tool section with the query criteria used to run

this previous query. Useful for rerunning of a previous query.

Rename: Renames the query to something more meaningful.

Remove: Removes the query from your list of previous queries. Note: history of this query still exists for auditing purposes.

Workplace The workplace is i2b2's equivalent to a storage location for: Query Definitions, Previous Query Results, and Concepts. Users each

will have their own personal folders for storing of these items. The "SHARED" folder is visible to all users, so it becomes useful at

times when you want to share your Previous Queries or Query Definitions with other users.

You can drag and drop queries from your "Previous Queries" section into your Workplace for use at a later time. When you use the

"Save Query Definition" feature in Query Tool, that definition gets stored in your personal folder. You can also drag concepts from

the Ontology tree down into the Workplace.

Getting Started Guide The Getting Started Guide is a handy reminder of how to use i2b2 to "build a patient cohort". There are several examples along with

detailed instructions.

i2b2 Training Manual 9

Query Verbalizer The query verbalizer is an extension of features from the Query Tool. As you build your query, the Getting Starting Guide

disappears, and the Query Verbalizer tab is activated. It provides an English description of what your query will return.

Creating a Simply Query Now that you are more familiar with the sections of the Workbench, let’s try a simple query. Suppose we wanted to search for

female patients who were diagnosed at some time with Myocardial Infarction.

The following are the steps to create your simple query:

i2b2 Training Manual 10 1. In the Ontology view, click on the plus sign to expand the Ontology folder.

2. Expand the Demographics folder and then expand the Gender folder.

3. Highlight the concept called Female by clicking on it.

4. While holding the left mouse button down, drag the concept to the Query Tool view - "Drag terms here" section at the

bottom of the first panel.

5. The concept will now appear in the first panel.

6. Back in the Ontology view, expand the Diagnoses folder located in the Ontology folder.

7. Once this folder opens, expand the Circulatory System folder

8. Highlight the Acute Myocardial Infarction folder

9. While holding the left mouse button down, drag the entire folder to the Query Tool view- "Drag terms here" section at the

bottom of the second panel

10. The folder will now appear in the second panel.

11. Click on the Run Query Above button.

12. The Query Name Dialog box will open.

i2b2 Training Manual 11

13. Name your Query or accept the default and click on the Run Query button.

14. When the query has completed the number of patients found matching the criteria will display in the Query Results box

below the Query Tool

15. The query will also save to the Previous Queries section under today’s date

i2b2 Training Manual 12 Advanced Query Let’s use the previous query as an example to get us started. In this Advanced option we are going to use the same simple query, but

limit our results to patients less than 10 years old.

1. In the second panel of the Query Tool section, Right-click on your Acute Myocardial Infarction Diagnosis concept folder.

2. You are given the options to:

a. Constrain by Value

b. Age at Event

3. Left-click (select) Age At Event

4. In the Age At Event window select the Operator "less than," leave the Unit as "Year(s)" and type the Age value of "10"

5. Click "Apply"

6. Click "Run Query"

7. Name your Query or accept the default and click on the Run Query button.

8. When the query has completed the number of patients found matching the criteria will display in the Query Results box

below the Query Tool

9. The query will also save to the Previous Queries section under today’s date

10. Note the different query result from our Simple Query

i2b2 Training Manual 13

Summary If you need additional assistance in utilizing i2b2, don't hesitate to email us at help-i2b2@bmi.cchmc.org. We will be sure to keep

you posted on any upcoming changes we have planned, such as new data domains or interface enhancements.

Please be sure to check back to our website https://i2b2.cchmc.org/ as well.