Welcome to Clinical Query 2 (CQ2)

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.
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.

Important notes about the Data Download Tool: 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). Note that, in most cases, protocols approved by other institutions (e.g., DFCI) are not sufficient to use the Data Download Tool. This is because of technical limitations in how auditing in CQ2 works and the data collected by the BIDMC electronic IRB system. We are working on a solution to this problem. 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.

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 each night from the CDR. However, there could be a 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.

COVID-19 nucleic acid and antibody test results can be found in the Aggregate Query Tool under Laboratory Tests > Other/Unclassified > Coronavirus.

The table below provides details on each of the sources of data for CQ2.

Data Type Coding Description
Demographics CQ2 Demographic data are obtained primarily from patient billing information, with BIDMC-specific codes consolidated into CQ2 categories, which include patient age, gender, and race. CQ2 contains demographic data for 2,983,185 patients.
Diagnoses ICD-9
ICD-10
Diagnoses are obtained from ED, inpatient, and outpatient (OMR) records. Both primary and secondary diagnoses are included in CQ2. CQ2 contains 58,183,192 diagnosis codes for 1,636,977 patients. Most diagnoses after October 1, 2015, use ICD-10 codes instead of ICD-9.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
6
3
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
20
10
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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Medications RxNorm Medications are obtained from both inpatient (POE) and outpatient (OMR) records. CQ2 contains 48,233,277 medication records for 963,836 patients. This represents 82% of the medications in the CDR. The remaining medications have not been mapped to RxNorm yet.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
4
2
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
20
10
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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Laboratory Tests LOINC Laboratory tests are obtained from inpatient and outpatient records. CQ2 contains 237,785,863 laboratory test results for 1,043,145 patients. This represents 95% of the laboratory test results in the CDR. The remaining tests have not been mapped to LOINC yet.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
20
10
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
100
50
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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Procedures CPT-4 Procedure codes are obtained from billing records. CQ2 contains 44,874,819 CPT-4 codes for 1,497,104 patients. CPT-4 codes for Pathology & Laboratory are currently not included in CQ2.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
4
2
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
20
10
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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ICD-9
ICD-10
CQ2 contains 7,331,925 ICD-9 procedure codes for 854,748 patients. Note that most procedures are only coded as CPT-4 starting January 1, 2010; and, ICD-10 replaced ICD-9 codes starting October 1, 2015.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
1
0.5
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
6
3
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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Vital Signs LOINC Vital signs are obtained from OMR sheet records. CQ2 contains 45,246,510 vital signs results for 676,123 patients starting in 2006.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records (Millions)
6
3
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Records / Patients
30
15
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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Visits   CQ2 contains data for 1,199,998 emergency visits for 494,705 patients.
Patients (Thousands)
60
30
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits (Thousands)
80
40
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits / Patients
2
1
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
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CQ2 contains data for 898,513 inpatient visits for 492,285 patients.
Patients (Thousands)
60
30
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits (Thousands)
60
30
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits / Patients
2
1
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
show table
CQ2 contains data for 34,745,577 outpatient visits for 1,431,527 patients.
Patients (Thousands)
400
200
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits (Millions)
4
2
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
Visits / Patients
8
4
0
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
95
00
05
10
15
20
Year
show table

Release History

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

Date Description
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.