Welcome to Clinical Query 2 (CQ2)

A new version of this website, BILH i2b2, is now available!
As of June 1, 2024, the data in Clinical Query 2 (CQ2) are no longer being updated. The new BILH i2b2 website contains both the historic BIDMC data from CQ2 as well as new data from Epic across all BILH locations. You can continue to use CQ2 if you need to access your previous queries since those cannot be copied over to the BILH i2b2 website. Note that the BILH i2b2 website is based on the same software as CQ2, but it has an updated look-and-feel. Please contact Griffin Weber at gweber@bidmc.harvard.edu if you have questions or feedback about the new website.

Clinical Query 2 (CQ2) is a website that allows you to search the BIDMC Clinical Data Repository (CDR) for research purposes, such as obtaining preliminary patient counts for a grant or IRB proposal. CQ2 contains two tools:

Feature Description
Aggregate Query Tool After entering inclusion and exclusion criteria, CQ2 will tell you the number of matching patients in the CDR. You do not need an IRB protocol to run these aggregate count queries. For additional patient privacy, a small random number is added to the actual number of matching patients and small counts are masked. Attempts to circumvent this might result in your CQ2 account being deactivated.
Data Download Tool If you have IRB approval, you can download patient level data, such as the medical record numbers (MRNs), for the patients who matched an aggregate count query that you previously ran in CQ2. By default, only Principal Investigators (PIs) of protocols approved by the BIDMC IRB can use the Data Download Tool; however, PIs can grant access to Co-Investigators (see instructions within the Data Download Tool). Please see the the section below on "Help and Support" for information on how the BIDMC InSIGHT Core can assist with accessing BIDMC clinical data.

Information about Epic: CQ2 is preparing for the transition to Epic! Users will still be able to access CQ2 after the Epic go-live, with new data for CQ2 coming from Epic. More information will be posted here over the next few months.

Begin Using CQ2

In order to use CQ2, you will first need to complete HIPAA training (if you have not done so already), and then login to the website using your ITS username and password.

Username      Password     

Help and Support

For questions about using CQ2, please contact Griffin Weber at gweber@bidmc.harvard.edu or Academic Computing at research@bidmc.harvard.edu.

The InSIGHT Core is a research core at BIDMC that was created to help investigators extract custom datasets from clinical systems at BIDMC. In particular, the InSIGHT Core can access data that are not in CQ2, and they can format the data in ways that are not possible through CQ2. The InSIGHT Core can also access the list of patients who matched a query you previously ran using the Aggregate Query Tool. To get started, please contact Karla Pollick from the InSIGHT Core at kpollick@bidmc.harvard.edu.

User Feedback

CQ2 is an evolving product. We continually add new data and features based on feedback from investigators. Please send your suggestions on how we can improve CQ2 to Griffin Weber at gweber@bidmc.harvard.edu.

CQ2 Database Status

The CQ2 database contains most, but not all of the data inside the BIDMC clinical data repository (CDR). Data are not included in CQ2 if they cannot be mapped to a standard medical coding system. This can occur due to data entry errors, missing data, the use of codes that are now obsolete, or other reasons. We will continue to improve the data mapping and add new types of data in the future.

New data are loaded into CQ2 about once a month from the CDR. However, there could be an additional delay of a month or more until certain types of clinical data enter the CDR. As a result, there will also be a delay in when these data appear in CQ2. Also, occasionally, older records in the CDR are modified, for example, to correct errors. There might be a time lag of a couple months until those modifications are reflected in CQ2.

Release History

The following dates indicate major updates to the Clinical Query 2 website:

Date Description
12/26/2021 The Aggregate Query Tool was updated with new features, including an improved Find Terms tool and new charts showing demographic breakdown results.
04/06/2018 PIs with IRB approved protocols can now authorize co-investigatrs to extract patient level data from the Data Download Tool.
12/31/2015 Diagnosis and procedure codes were updated to support the switch from ICD-9 to ICD-10 that occurred on October 1, 2015.
04/28/2015 A Data Download Tool was added to CQ2 to enable investigators who have IRB approval to extract patient level data.
02/10/2015 The CQ2 home page was expanded to include release history and display the number of patients per year with each data type. New functionality includes temporal queries, demographic breakdowns on query results, and a new Workplace section to bookmark commonly used concepts or save previous queries.
10/28/2014 Vital signs were added.
08/18/2013 Visit details (emergency, inpatient, outpatient, length of stay) were added. Users can now search for concepts that were observed in the same financial encounter.
10/01/2012 CQ2 was launched.