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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. |
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.
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.
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.
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 3,328,740 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 73,700,964 diagnosis codes for 1,896,107 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
|
Medications | RxNorm | Medications are obtained from both inpatient (POE) and outpatient (OMR) records. CQ2 contains 56,819,162 medication records for 1,120,028 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
|
Laboratory Tests | LOINC | Laboratory tests are obtained from inpatient and outpatient records. CQ2 contains 303,253,611 laboratory test results for 1,296,795 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
|
Procedures | CPT-4 | Procedure codes are obtained from billing records. CQ2 contains 56,855,511 CPT-4 codes for 1,699,919 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
|
ICD-9 ICD-10 |
CQ2 contains 7,586,602 ICD-9 procedure codes for 896,540 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
|
|
Vital Signs | LOINC | Vital signs are obtained from OMR sheet records. CQ2 contains 57,872,905 vital signs results for 799,498 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
|
Visits | CQ2 contains data for 1,362,426 emergency visits for 554,876 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
|
|
CQ2 contains data for 1,016,399 inpatient visits for 555,297 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
|
||
CQ2 contains data for 42,318,588 outpatient visits for 1,678,256 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
|
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. |