Please refer to attached documents.
Data Source/clinical domain:
Files:
People Watching For Updates:
Suggested Citation
Ning Sunny Shang. Mayo Clinic. Cardiorespiratory Fitness Algorithm (eMERGE Mayo Network Phenotype). PheKB; 2012 Available from: https://phekb.org/phenotype/125
David Carrell
CRF NLP system availability?
Mon, 2013-04-01 12:29Hi,
Any information on when the NLP component for the CRF algorithm will be ready? Of, if it is ready now, where we can download it?
Thanks,
David Carrell (Group Health)
Jen Pacheco
data dictionary with min-max expected, etc.
Mon, 2013-04-22 13:17Can you please upload a data dictionary that follows the format eMERGE uses, which includes:
This will help us to know where to cut off our values, and will help you to have standardized variable names.
:)
Thank you!
Northwestern
Jen Pacheco
3 data dictionary questions
Thu, 2013-04-25 17:38Jen Pacheco
2 more data dictionary questions about meds for clarification
Fri, 2013-04-26 15:15Jyoti Pathak
Updated CRF data dictionary
Tue, 2013-05-14 21:00Hi everyone, we have updated the CRF data dictionary consistent with the standardized data elements in eleMAP. That said, there are many data elements specific to CRF that are not available via caDSR or other resources. Please review, and let us know if there are any further questions. Thanks, Jyoti
David Carrell
Medication Data for CRF
Wed, 2013-05-15 08:46Medication data are to be provied for the period +/- 6 months from the reference date (which is earliest CRF test). Is the data for each individual drug dispensed to be provided as "ever/never" or do you want multiple records indicating each time each individual drug was dispensed in that 12-month period?
Jyoti Pathak
Medication data for CRF
Wed, 2013-05-15 10:49Davoid, we need the "ever/never" information only. Thanks, Jyoti
Jyoti Pathak
Medication data for CRF
Wed, 2013-05-15 10:49David, we need the "ever/never" information only. Thanks, Jyoti
David Carrell
Medication data for CRF
Mon, 2013-09-16 18:40Since these data are indicating "ever/never" exposure to the drug within the period 6 months +/- the exercise test date, it would seem that you do not really need the subject's age at medication date, since you already have the subject's age at exercise test date. Do you agree? If you still want subject age at medication date, which date should we use when multiple medication orders/fills are present within the period? The earliest? The latest? Thanks, -David
Jouni Hayan
Hi David,
Tue, 2013-09-17 09:50Hi David,
Since we already have the age given the test date and date of birth, there's no need to look at age at the time of the medication. Basically, we need to know whether a patient was on any of these medicaitons in the time period of +/- 6 months around the exercise test date.
Thanks,
Hayan
David Carrell
Great. Thanks.
Tue, 2013-09-17 11:15Great. Thanks.
Jen Pacheco
Which codes or algorithms for last 3 comorbid conditions?
Mon, 2013-05-20 15:24For the following variables,
are there ICD-9 codes
and/or
algorithms we should use (still none specified in the posted documents that we could find)?
If so, which codes or which algorithms?
Jyoti Pathak
Jen, thanks for the questions
Tue, 2013-05-21 18:13Jen, thanks for the questions. I have added the list of codes for the co-morbidities. Please see updated Data Dictionary (and the new tabs in the XLS file). Thanks, Jyoti
Arun Muthalagu
co-morbidities code list
Wed, 2013-05-22 15:06We had earlier used code list in the algorithm document (word file) , the updated data dictionary (XLS) code list are different for few co-morbidities. Do you want us to use the data dictionary code list?
Jyoti Pathak
Yes, please use the codes in
Wed, 2013-05-22 15:21Yes, please use the codes in the updated data dictionary XLS file. Thanks, Jyoti
David Carrell
Comorbidity dx code matching
Wed, 2013-09-04 16:41We have noticed that matching for the explicit codes (e.g., 411.81, 411.89, etc.) is a more precise method than matching for the code with wildcard characters (e.g., 441.xx). I mention this because the wildcard version of the codes are in the pseudocode document, but it is probably best not to use them.
David Carrell
"Rule of two" dx codes -- applies only to 5 of 8 comorbidities?
Wed, 2013-09-04 18:41Hi,
There are eight comorbidities listed in the data dictionary (and pasted below). The first five in this list use a "rule of two" (i.e., the dx codes must appear on at least two separate calendar dates during the specified 12-month period in order for the comorbidity flag to be set to true). The last three comorbidities simply say the dx must be "present" in the period. Should the last three comorbidity flags really be calculated differently than the first five?
Coronary heart disease
Congestive heart failure
Cardiomyopathy
Peripheral arterial disease
Chronic Obstructive Pulmonary Disease
Hypertension
Dyslipidemia
Diabetes_Mellitus
Thanks,
David
David Carrell
Variable names with embedded spaces (some quite long)
Wed, 2013-09-04 19:07Hi,
Most of the variable names in the CRF data dictionary seem reasonable. However, some are quite long and have embedded spaces (as shown in the lists below). Do you really want us to use these exact variable names in the datasets we provide?
VARNAMEs on Basic data tab:
=====================
SUBJID
Sex
Year_Birth
Observation_age
Race
Ethnicity
Coronary heart disease
Congestive heart failure
Cardiomyopathy
Peripheral arterial disease
Chronic Obstructive Pulmonary Disease
Hypertension
Dyslipidemia
Diabetes_Mellitus
Smoking_Status
VARNAMEs on Exercise test data tab:
==========================
SUBJID
Exercise_test_date
Test type
Exercise type
Protocol type
METs
Exercise time
Blood pressure at REST
Blood pressure at PEAK
Heart rate at REST
Heart rate at PEAK
Peak VO2
VE/VCO2 Nadir
Anaerobic threshold
Thanks,
David
David Carrell
Name of variable for recording conditions S1-S5?
Thu, 2013-09-05 17:33Hi,
The pseudocode algorithm document says we should provide the flag variable for each subject defined as S1, S2, S3, S4 or S5 (per the pasted text below). What do you want to name that field? I don't see it listed in the data dictionary.
Thanks,
David
S1: ECG (any of the CPT-4 codes: 93015; 93016; 93017; 93018) + Echo (CPT-4 code 93350); OR Echo code 93351 only;
S2: ECG (any of the CPT-4 codes: 93015; 93016; 93017; 93018) + Cardiac nuclear test (CPT-4 codes: A9500);
S3: ECG (any of the CPT-4 codes: 93015; 93016; 93017; 93018) + Oxygen uptake (any of the CPT-4 codes: 94680; 94681);
S4: ECG (any of the CPT-4 codes: 93015; 93016; 93017; 93018) only.
S5: If the patient is flagged as S1 and S3 simultaneously, set that patient as S5.
David Carrell
Calendar date data format
Thu, 2013-09-05 22:21Hi,
The data dictionary calls for some calendar dates (e.g., Exercise_test_date). What is the format of these dates? The dictionary simply says "numeric" but more details are needed. Do you want to use the SAS numeric representation of a date? Excel's numeric representation? MS SQL Servers? Or, perhaps, do you want us to provide dates in a standardized text format? I believe we discussed this in the past and were leaning toward a standardized string representation of dates (e.g., YYYYMMDD or YYYY-MM-DD). Please clarify.
Thanks,
David
Jyoti Pathak
Hi David - for the sake of
Fri, 2013-09-06 12:05Hi David - for the sake of simplicity, lets use YYYY-MM-DD. Thanks, Jyoti
David Carrell
dates
Fri, 2013-09-06 12:33Perfect. Thanks.
Jouni Hayan
Hi David,
Mon, 2013-09-09 12:03Hi David,
Thanks for your help with this phenotype. Please find responses below in bold.
Please feel free letting us know if you have any other questions.
Thanks again!
Hayan
1. We have noticed that matching for the explicit codes (e.g., 411.81, 411.89, etc.) is a more precise method than matching for the code with wildcard characters (e.g., 441.xx). I mention this because the wildcard version of the codes are in the pseudocode document, but it is probably best not to use them
Let's stick to the codes listed in the data dictionary since we already extracted the data based on them.
2. Most of the variable names in the CRF data dictionary seem reasonable. However, some are quite long and have embedded spaces (as shown in the lists below). Do you really want us to use these exact variable names in the datasets we provide
Agree, you can use abbreviated terms as below:
VARNAMEs on Basic data tab:
=====================
SUBJID OK
Sex OK
Year_Birth OK
Observation_age Obs_age
Race OK
Ethnicity OK
Coronary heart disease CAD or CHD
Congestive heart failure CHF or HF
Cardiomyopathy CMP
Peripheral arterial disease PAD
Chronic Obstructive Pulmonary Disease COPD
Hypertension HTN
Dyslipidemia HPL
Diabetes_Mellitus DM
Smoking_Status Smoking
VARNAMEs on Exercise test data tab:
==========================
SUBJID
Exercise_test_date Test_dt
Test type Test_type
Exercise type Exer_type
Protocol type Protocol
METs OK
Exercise time Exer_time
Blood pressure at REST Please separate into: Rest_SBP (for systolic blood pressure) and Rest_DBP (diastolic BP)
Blood pressure at PEAK Again Peak_SBP and Peak_DBP
Heart rate at REST Rest_HR
Heart rate at PEAK Peak_HR
Peak VO2 Peak_vo2
VE/VCO2 Nadir VE_VCO2_nad
Anaerobic threshold Anaerob_thresh
3. There are eight comorbidities listed in the data dictionary (and pasted below). The first five in this list use a "rule of two" (i.e., the dx codes must appear on at least two separate calendar dates during the specified 12-month period in order for the comorbidity flag to be set to true). The last three comorbidities simply say the dx must be "present" in the period. Should the last three comorbidity flags really be calculated differently than the first five?
Coronary heart disease
Congestive heart failure
Cardiomyopathy
Peripheral arterial disease
Chronic Obstructive Pulmonary Disease
Hypertension
Dyslipidemia
Diabetes_Mellitus For the last three variables hypertension, dyslipidemia, and diabetes, only one code +6 mo/ -6 mo from the time of the test is sufficient to mark as present. The other variables F1 through F5 need 2 codes.
4. The pseudocode algorithm document says we should provide the flag variable for each subject defined as S1, S2, S3, S4 or S5 (per the pasted text below). What do you want to name that field? I don't see it listed in the data dictionary? Yes please. We will need to know the exact types of tests. Please create fields S1 through S5 and mark as Y for every patient based on the stress modality they had.
5. Regarding the test date, I agree with Jyoti.
Ken Borthwick
Questions about new Data Dictionary
Thu, 2016-08-18 10:48Thank you for providing data dictionaries in the new format. I have some questions about eMERGE_DD_CRF_Exercise_data_5_24_2016_v6_0. First, peak blood pressure is listed as one field. Could you please split that into two fields? Second, the field Exercise_ECG doesn't have a description. What does that field represent? Could you add a description please?
Thank you,
Ken
Jouni Hayan
We apologize for the late
Thu, 2016-12-08 09:08We apologize for the late reply. Peak blood pressure would be peak systolic blood pressure. If getting the peak diastolic pressure is easily obtainable, please include that as well. Exercise ECG should be either 0=Negative; 1=positive; 2=abnormal & non-diagnostic for ischemia; .=missing/unknown/unassessed/non-applicable.
Thanks,
Hayan
Jouni Hayan
We apologize for the late
Thu, 2016-12-08 09:08We apologize for the late reply. Peak blood pressure would be peak systolic blood pressure. If getting the peak diastolic pressure is easily obtainable, please include that as well. Exercise ECG should be either 0=Negative; 1=positive; 2=abnormal & non-diagnostic for ischemia; .=missing/unknown/unassessed/non-applicable.
Thanks,
Hayan