User s s Guide and v1.3
Contents General Information... 3 Q: What is i2b2?... 3 Q: How is i2b2 populated?... 3 Q: How often is i2b2 updated?... 3 Q: What data is not in our i2b2?... 3 Q: Can individual patients be identified?... 3 Q: Do I need IRB approval to use the de-identified i2b2?... 3 Q: What if I want to find out actual patient information?... 3 Q: What are the system requirements for the i2b2 web client?... 4 Q: How do I access the i2b2 web client?... 4 System Navigation... 4 Q: What are the available sections in the i2b2 web client?... 4 Q: What are the icons at the top of each window?... 5 Term Search... 6 Q: How do I search for a term?... 6 Q: Is there support for using wildcards in search?... 7 Query Building... 7 Q: How do I build a query?... 7 Q: How do I distinguish between Or and And?... 8 Q: How do I use the Dates function?... 9 Q: Do I have to use the Dates function?... 10 Q: Can I use different dates for each group?... 10 Q: How do I use the Occurs function?... 10 Q: How do I use the Exclude function?... 11 Q: Can a query time out?... 12 Q: The results indicate that there are 0 patients, but I know patients in our system should meet the search criteria what s going on?... 12 Saved and Previous Queries... 13 Q: How do I see the results of a previous query?... 13 Q: How do I re-run a previous query?... 13 Q: How do I save a query?... 13 Q: How do I create a new folder in my Workplace folder?... 14 Q: How do I re-run a saved query?... 14 Q: Can Managers see all queries?... 14 Q: What should I keep in mind when building queries?... 15 2 2012 Cerner Corporation. All rights reserved. This document contains Cerner confidential and/or proprietary information which may not be reproduced or transmitted without the express written consent of Cerner.
General Information Q: What is i2b2? i2b2 (Informatics for Integrating Biology & the Bedside) is an informatics framework created through NIH funding to leverage existing data for research cohort discovery. i2b2 was designed to support cohort identification, retrospective data analysis, and hypothesis generation. i2b2 consists of a workbench and a web client. The i2b2 web client is designed with a user-friendly, drag-and-drop interface to enable users to perform these tasks without extensive training or technical expertise. The i2b2 workbench is a desktop-based application that can also interface with i2b2 data, but is designed to accommodate more frequent i2b2 users. Q: How is i2b2 populated? i2b2 is populated using Cerner s Health Data Architecture. Leveraging a nightly extraction process, our institution sends data from the Cerner Millennium EMR, along with associated data, for mapping into a data mart that feeds i2b2. Q: How often is i2b2 updated? Cerner i2b2 is updated daily. Q: What data is not in our i2b2? Religion, Language Age at encounter (note: Age is calculated based on the date the query is run. Therefore, to do a query of patients with a specific age restriction, it is necessary to extrapolate to what age would be today) Provider data Vital signs and other non-laboratory clinical events Microbiology data or anything else not available in PI Q: Can individual patients be identified? Your institution has access to 2 separate i2b2 instances: De-identified project and Identified project. Access is granted by an Administrator, and most users will only have access to the de-identified project type. Q: Do I need IRB approval to use the de-identified i2b2? Cerner recommends confirming this with the local IRB. If the HRRC gives a determination that data in the deidentified i2b2 project is not PHI, then you can use the de-identified project of i2b2 once you have been granted access without any further approvals by the IRB. Q: What if I want to find out actual patient information? An honest broker will access the identified project, with appropriate IRB approval, much like the process for requesting data from the CDW. A well-formed query that has been performed on the de-identified project will facilitate the retrieval of identified information. 3 2012 Cerner Corporation. All rights reserved. This document contains Cerner confidential and/or proprietary information which may not be reproduced or transmitted without the express written consent of Cerner.
Q: What are the system requirements for the i2b2 web client? The i2b2 web client is compatible with multiple platforms (Windows & Mac) and browsers (Firefox, Internet Explorer, Safari, and Google Chrome). While all platforms are compatible, Firefox and Google Chrome are preferred for an optimal user experience. Q: How do I access the i2b2 web client? The i2b2 web client can be accessed at the following address: https://i2b2.cernerresearch.com/webclient/# 1. Enter your Username (CASE SENSITIVE) 2. Enter your password (remove the default password) 3. Leave i2b2 Host defaulted to: Cerner Research 4. Click Login 5. If prompted with the Choose a Project window, select the desired Project and click Go. Note: Some users will have access to multiple i2b2 Projects. Contact your i2b2 administrator for details. System Navigation Q: What are the available sections in the i2b2 web client? After logging into the i2b2 project, you will be presented with the following screen: The main i2b2 screen displays the following sections: 4 System Navigation 2012 Cerner Corporation. All rights reserved. This document contains Cerner
A. Navigation tabs These tabs have 2 possible selections: i. Navigate Terms This allows the user the ability to navigate the entire i2b2 ontology. (see Ontology Explorer for more details). ii. Find Terms This allows the user to search based on naming convention or actual code value. B. Ontology Explorer The Ontology Explorer allows the user to navigate the entire Ontology of i2b2. C. Workplace Contains saved directories. Users can either save or share previous queries here. D. Previous Queries This section contains most recently run queries. E. Query Tool The Query Tool is used to build query concepts. The Query Tool contains group panels, each indicating a separate term or term group you wish to be included in your query. F. Query Status The Query Status contains the execution status of any query currently being run. G. Toolbar The toolbar includes the following links: i. Find Patients Clicking this link directs the user back to the main i2b2 query tool ii. Analysis Tools Clicking this link directs the user to the Plugin Viewer. Currently, only example plugins are loaded. iii. Message Log The message log is intended to provide detailed information about i2b2 s performance for troubleshooting. iv. Help Clicking this link accesses the basic i2b2 Help page. v. Logout Clicking this link logs the user out of the system. Q: What are the icons at the top of each window? Windows in the i2b2 web client contain multiple icons to control the display and contents of the window. The first icon will display the XML Message Stack. This window can be used for debugging and technical troubleshooting. 5 System Navigation 2012 Cerner Corporation. All rights reserved. This document contains Cerner
Clicking the second icon (if available) will display options for that specific window. Here, users can adjust options like the sorting format for previous queries. Clicking the last icon will expand the window to its maximum size. Term Search Q: How do I search for a term? i2b2 enables users to search for terms, to supplement the use of the Ontology explorer. The Find Terms window allows for searches by term name and code. To search by term name, click the Find Terms navigation tab, and ensure that Search by Names is selected. Using the contains search will perform a search to find the search term text in any term in the Ontology. i2b2 makes other searches possible. For example, like the exact search, which will only return results that perfectly match the search criteria and the left search which will return results that contain the text string at the start of the word or phrase. Click Find when you have completed entering your search criteria. To search by code, click the Find Terms navigation tab, and then select the Search by Codes tab. Here, you must enter a code and select a coding system (examples: ICD-9, NDC, SNOMED). Click Find when you have completed entering your search criteria. 6 Term Search 2012 Cerner Corporation. All rights reserved. This document contains Cerner
Q: Is there support for using wildcards in search? Today, the i2b2 application does not support the use of wildcard expressions (*,%, etc.) in searching. While not exactly synonymous, it is possible to perform a contains search to query the ontology for all terms that contain a substring of text. Query Building Q: How do I build a query? Queries can be built using i2b2 s simple drag and drop interface. Once you have identified a term that you wish to query for, simply click and drag the term over to Group 1 in the Query Tool. Once a single term is entered into the group, the second group becomes enabled and is available to be utilized. A second term can be added to the group. Once the query has been developed, click Run Query at the bottom of the Query Tool. 7 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
You will then be asked to name the query. By default, the query will be named with an abbreviated version of the terms and the time the query was run. The name can be changed by editing this text. You will also be asked whether you would like to generate a Patient Count or a Patient Set. Generating a patient count will yield an aggregate number of patients that meet the query criteria. Generating a patient set will yield the ability to create a list of all patients that meet the query criteria. Please note, only users with Limited Data Set or Protected data access roles will be able to generate patient set lists; those with Obfuscated or Aggregated permissions can only generate patient counts. Click OK to run the query. The query will execute as designed. Check the Query Status window for information as the query runs. When the query completes, you will be given the number of patients that meet the search criteria and the time taken to run the query. Note: Users with Obfuscated permissions will retrieve results that are obfuscated (obscured) by returning +/- 3 records each time the query is run. These users are also limited to the number of times they can run the same query in a predefined time period. All other data access roles will retrieve exact query results. Q: How do I distinguish between Or and And? Building a group of terms across the group panels naturally indicates an And connector. For example, the following query indicates a query for females who have had a Cesarean section and have a diagnosis of essential hypertension. 8 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
To build a query with Or, simply include the terms in the same group panel. For example, to query for females who have had a Cesarean section OR have a diagnosis of essential hypertension, build the query like this: In i2b2, this will query for females who have at least one or more of the criteria in Group 2. Females who are hypertensive and have given birth via Cesarean section will meet the criteria of this query. Q: How do I use the Dates function? In i2b2, the Dates function can be used to further refine the query to only include terms that have been recorded during a specific time. The Dates function can be used for activities data, like visits, medications, procedures and diagnoses. Note: Reference data, like demographics, will not be compatible with the Dates function. If the Dates function is used with reference data, it will retrieve 0 patient results. The Date function i2b2 allows users to set a beginning date, an end date, or both. For example, if you wanted to query for patients who have had an Obstetrical Procedure (ICD-9 72-75) since January 1, 2012, with no particular end date, follow these steps: 1. Once the desired term has been input into the group panel, click the Dates button. 9 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
2. On the Date Range pop-up, enter the dates you would like to restrict your query to. For this example, select the check-box for From: to indicate you will be setting a beginning date, and enter 01/01/2012. i2b2 displays dates in the MM/DD/YYYY format. 3. Click OK. The date range has now been set. When the query is run, i2b2 will only return patients who have had an Obstetrical Procedure since January 1, 2012. Q: Do I have to use the Dates function? No, the use of the Dates function is optional. If a query term is not date-limited, i2b2 will return all results for that term, regardless of date. Q: Can I use different dates for each group? Yes. Each group has a unique Dates function. For example, if you build a query with a first group with an Obstetrical Procedure term and a date limitation of 01/01/2012 12/31/2012, and a second group with the Essential Hypertension term and no date limitation, i2b2 will return the number of patients who had have a diagnosis of essential hypertension recorded at some point in i2b2 and an Obstetrical Procedure recorded in 2012. Q: How do I use the Occurs function? In i2b2, the Occurs function allows users to query for patients with multiple occurrences of a term. For example, to search for a patient with more than one Obstetrical Procedure (ICD-9 72-75), follow these steps: 1. Once the desired term has been input into the group panel, click the Occurs > 0x button. 10 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
2. On the Occurrences pop-up, select the number of term occurrences you require in your query. For this example, select 1. 3. Click OK. The occurrence limit has now been set. When the query is run, i2b2 will only return patients who have at least two Obstetrical Procedures. Q: How do I use the Exclude function? In i2b2, the Excludes function allows users to exclude a group of patients from a query. For example, to query for all patients who have had an Obstetrical Procedure except for patients with a Low cervical cesarean section (ICD-9 74.1), follow these steps. 1. Build a query with multiple group panels. One panel should include the group you wish to exclude from your query. For this example, the below query can be built. 2. Once the desired term of exclusion has been input into the group panel, click the Exclude button. 11 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
3. The label on the group panel will change to say none of these. When the query is run, i2b2 will return all patients with an Obstetrical Procedure, except for patients with a Low cervical cesarean section. 4. An alternate way to toggle exclusion criteria is to click the Excludes label on the group panel. To add exclusion criteria, the panel will change from all of these to none of these. To remove exclusion criteria, it will change from none of these to all of these. Q: Can a query time out? Queries do not time out in i2b2. They will always run to completion, as long as the application is connected to the database. Most queries run in under one minute. In the event that a query is particularly large (either in scope of terms, or scope of patients potentially returned), queries may run longer. The i2b2 web client will eventually display a message (after 5 minutes) indicating that your session has expired, but the query will continue. Simply log back into the application and check the Previous Queries window for your results. In the event that a query does not ever return, please contact your i2b2 administrator. Q: The results indicate that there are 0 patients, but I know patients in our system should meet the search criteria what s going on? There are a number of explanations for this scenario. 1. For HIPAA compliance reasons, i2b2 obfuscates results below a threshold for some roles. With the obfuscated data protection role, the query count can be configured to prevent retrieving results lower than a certain threshold. This may be configured if there is concern that results lower than this threshold could result in patient re-identification. 2. It is possible that one or more patients are not properly documented in the Cerner Millennium EMR. 3. <Hold for future information about limited data, i.e. Lab/Micro> 12 Query Building 2012 Cerner Corporation. All rights reserved. This document contains Cerner
Saved and Previous Queries Q: How do I see the results of a previous query? i2b2 automatically saves the results of previous queries. The Previous Queries window maintains a list of queries run recently, and displays them by Query Name given at the time of the initial run. To view the results of a previous query, simply expand the Query Name folder, which will reveal the results folder. Expand the results folder, which will reveal the Patient Count and/or Patient Set that was generated. Q: How do I re-run a previous query? To re-run a query, simply drag the Query Name folder back onto the Query Tool. The Query Tool will populate with the group panels that were originally selected. Click Run Query. Note: Previous queries can be refined once a user drags the query into the Query Tool. Q: How do I save a query? While i2b2 saves previous queries for future reference, older queries eventually are removed from the list. To permanently save the query for your future reference, drag the Query Name folder into the Workplace window 13 2012 Cerner Corporation. All rights reserved. This document contains Cerner confidential and/or proprietary information which may not be reproduced or transmitted without the express written consent of Cerner.
onto your Username folde Q: How do I create a new folder in my Workplace folder? To create a new folder, right-click on the Username Workplace folder and click New Folder. Q: How do I re-run a saved query? To re-run a saved query, drag the Query Name folder from the Workplace window back onto the Query Tool. The Query Tool will populate with the group panels that were originally selected. Click Run Query. Note: Saved queries can be refined once a user drags the query into the Query Tool. Q: Can Managers see all queries? Yes. Users with the i2b2 Manager role can see all queries. 14 Saved and Previous Queries 2012 Cerner Corporation. All rights reserved. This document contains Cerner confidential and/or proprietary information which may not be reproduced or transmitted without
i2b2 Tips Q: What should I keep in mind when building queries? 1. There may be multiple queries to help address the same research question. To truly visualize the whole picture of a potential cohort, individually query for all possible associated medications, procedures, and diagnoses of the cohort. 2. Don t use the Dates or Occurs > 0x controls for person information. Person/demographic information like gender and race are not associated with specific dates. i2b2 will yield 0 results if group panels with person-specific information are date-limited. 3. Most queries finish in under a minute. To calculate the patient counts for parent concepts like Obstetrical Procedures, i2b2 will calculate all underlying terms. These queries tend to take a little longer. If a query seems to run indefinitely, contact your i2b2 administrator. 4. Other information may be developed on data limitations (0 patients vs. no data)> 15 i2b2 Tips 2012 Cerner Corporation. All rights reserved. This document contains Cerner