Data Dictionary `v1`

File Tree

datasets/
└── mrkr-emory-xray/
    ├── v1/
    │   ├── MRKR_CPT.csv
    │   ├── MRKR_CPT_dictionary.csv
    │   ├── MRKR_ICD.csv
    │   ├── MRKR_ICD_dictionary.csv
    │   ├── MRKR_pain.csv
    │   ├── MRKR_demographics.csv
    │   ├── MRKR_image_metadata.csv
    └── xray/
        ├── ...
        ...

Patient Demographics

Filename: MRKR_demographics.csv
Rows: 83,011
Columns: 4

This files contains patient demographics, indexed at the patient level.

Field Name	Data Type	Description
empi_anon	integer	Unique patient identification number (8 digits)
sex	nominal string	Patient sex `male` `female`
race	nominal string	Patient self-reported race `African American or Black` `American Indian or Alaskan Native` `Asian` `Caucasian or White` `Multiple` `Native Hawaiian or Other Pacific Islander` `Unknown`
ethnicity	nominal string	Patient self-reported ethnicity `Hispanic patients` `Non-Hispanic patients` `Unknown` `Unreported`

X-ray Image Metadata

Filename: MRKR_image_metadata.csv
Rows: 503,261
Columns: 19

This file contains relevant public DICOM metadata tags that may be helpful for identifying images. Patient and exam identifiers are replaced with de-identified versions in this table and within DICOM files. Other Non-PHI containing metadata tags that are not in this table are left intact within DICOM files. Fields containing PHI such as patient name, addresses, or referring physician are removed from this table and DICOM files. For data curation, the below fields were modified or added.

Field Name	Data Type	Description
empi_anon	integer	Unique patient identification number (8 digits)
StudyInstanceUID_anon	string	De-identified Study UID, shared between all images in the same study
SeriesInstanceUID_anon	string	De-identified Series UID, shared between all images in the same series
SOPInstanceUID_anon	string	De-identified SOP Instance UID which corresponds to a single DICOM image
img_height	integer	Image pixel height
img_width	integer	Image pixel width
laterality	nominal string	Laterality of the image, as inferred by DL model `R`: Right `L`: Left `B`: Bilateral `-1`: Unknown or not present
view_position	nominal string	Anatomical projection of radiograph, as inferred by DL model `F`: Frontal `L`: Lateral `S`: Sunrise `I`: Internal Oblique `E`: External Oblique
horizontal_flip	binary	Indicates if the patient’s left side was oriented to the left side of the image, which is opposite of typical radiographic orientation, as inferred by DL model.
weight_bearing	binary	Indicates if the radiograph was weight-bearing as indicated by a marker and derived by DL model. Not all images in a given exam will be weight-bearing or non-weightbearing.
inverted	binary	Indicates whether pixel intensity values are inverted from typical radiographic convention, as inferred by DL model.
arthroplasty	nominal string	Indicates if image contains a knee arthroplasty and its laterality, as derived by DL model. Applies to unilateral and bilateral view. `R`: Right `L`: Left `B`: Bilateral `NL`: Unknown (no laterality marker) `NaN`: No arthroplasty
L_KLG_inference	ordinal integer	KLG score of left knee in a bilateral knee radiograph, inferred by DL model [0-4]
R_KLG_inference	ordinal integer	KLG score of right knee in a bilateral knee radiograph, inferred by DL model [0-4]
SeriesDescription	string	DICOM Metadata describing the series
StudyDescription	string	DICOM metadata describing the study
StudyDate_anon	date	De-identified date of radiograph
age_at_exam	integer	Age of the patient when the radiograph was performed
dicom_path	string	Path to DICOM file

Pain Scores

Filename: MRKR_pain.csv
Rows: 4,975,933
Columns: 6

This file contains information on self-reported pain scores by patients during any, encounter, inculding outpatient, emergency, and perioperative. Pain scores related to knees are curated.

Field Name	Data Type	Description
empi_anon	integer	Unique patient identification number (8 digits)
pain_location	string	Raw, uncurated strings of pain locations entered by staff. Approximately 75% of entries are blank.
knee_pain	binary	Curated using regular expressions to identify if the pain_location is definitely knee related.
pain_score	integer	0 - 10 pain score
laterality	nominal string	`R`: Right `L`: Left `B`: Bilateral `NaN`: Unknown or not present Value only present if knee_pain is 1
date_anon	date	Date of when the pain score was entered into the patient’s chart.

Procedure Records

Filename: MRKR_CPT.csv
Rows: 6,216,190
Columns: 5

This file contains procedural codes for patients with corresponding dates.

Field Name	Data Type	Description
empi_anon	integer	Unique patient identification number (8 digits)
cpt_code	string	Current Procedural Terminology code used in coding of medical services and procedures for billing (5 characters) 7,166 CPT unique codes
cpt_group_modifier	string	Used to provide further information regarding service or procedure. Most CPT codes do not include modifier data. If there is modifier data, it is often used to indicate the laterality of a procedure (left or right). There can be multiple modifiers for a single CPT code entry. This field combines all of the modifiers for that particular CPT code for that specific encounter for that patient.
date_anon	date	Date of when the associated procedure or service occurred.
age_at_procedure	integer	Age when the procedure was performed

Procedure Code Descriptions

Filename: MRKR_CPT_dictionary.csv
Rows: 7,166
Columns: 2

This file contains descriptions of each Current Procedural Terminology (CPT) code found in MRKR_CPT.csv table.

Field Name	Data Type	Description
cpt_code	string	Current Procedural Terminology code used in coding of medical services and procedures for billing - (5 characters)
cpt_description	string	Description of the procedure. There are some unique CPT codes that share the same description. This leads to 128 fewer unique descriptions compared to unique CPT codes.

Diagnosis Records

Filename: MRKR_ICD.csv
Rows: 21,956,056
Columns: 16

This file contains diagnosis codes for patients with corresponding dates. Certain diseases of interest are indicated by binary flags to ease data cleaning.

Field Name	Data Type	Description
empi_anon	integer	Unique patient identification number (8 digits)
ICD9	string	International Classification of Diseases - 9 12,418 unque codes
ICD10	string	International Classification of Diseases - 10 26,963 unique codes
date_anon	date	Date when the diagnosis code was entered.
age_at_dx	integer	Age when the diagnosis was recorded.
DX_LINE	string	`Primary`, `Secondary`, `Active`, `Not Recorded`, `Resolved`, `Canceled`, `Inactive`
DX_ICD_SCOPE	string	`Billing Diagnosis`, `Discharge Diagnosis`, `Admitting Diagnosis`, `Referring Diagnosis`, `Not Recorded`, `Reason For Visit`, `Problem List`, `Working Diagnosis`, `Other Diagnosis`, `Final`, `Pre-Op Diagnosis`, `Post-Op Diagnosis`, `Principal Diagnosis`, `Suggested Billing`
autoimmune	binary	If ICD code corresponds to auto-immune disease such as rheumatoid arthritis, juvenile arthritis, gout, etc.
diabetes	binary	If ICD code corresponds to type I or type II diabetes
hypertension	binary	If ICD code corresponds to hypertension
joint_infection	binary	If ICD code corresponds to a knee joint infection
knee_osteoarthritis	binary	If ICD code corresponds to knee osteoarthritis
knee_osteomyelitis	binary	If ICD code corresponds to knee osteomyelitis
obesity	binary	If ICD code corresponds to knee obesity
nicotine_use	binary	If ICD code corresponds to nicotine dependence
trauma_lower_extremity	binary	If ICD code corresponds to lower extremity

Below is a description of the diseases of interest from the diagnosis table. This table shows the ICD9 and ICD10 prefixes used to flag these diseases along with frequency they are appear in the diagnoses codes.

DX Category	DX Entries in Category	Patients with DX in Category	ICD10 Prefixes	ICD9 Prefixes
autoimmune	122,859	9,704 (11.7%)	M05, M06, M08, M10, M45, M1A	274, 714, 720
diabetes	552,208	18,655 (22.47%)	E08, E10, E11, E13	250
hypertension	1,209,572	45,300 (54.57%)	I10-I16	401-405
joint_infection	2,224	551 (0.66%)	M00.06, M00.16, M00.26, M00.86, M01.X6, M02.06, M02.16, M02.26, M02.36, M02.86	711.06, 711.16, 711.26, 711.36, 711.46, 711.56, 711.66, 711.76, 711.86, 711.96
knee_osteoarthritis	373,186	51,468 (62.0%)	M17	715.16, 715.26, 715.36, 715.96
knee_osteomyelitis	7,130	1,389 (1.7%)	M86 related to thigh and tibia/fibula	730 related to lower leg
obesity	197,094	27,576 (33.2%)	E66.01, E66.09, E66.1, E66.3, E66.8, E66.9	278.0, 278.00, 278.01, 278.02
nicotine_use	148,095	20,882 (25.2%)	F17, Z57.31, Z71.6, Z72.0, Z77.22, Z87.891	305.1
trauma_lower_extremity	152,377	34,230 (41.2%)	S82.0, S82.1, S83	959.7, 844, 823, 891, 822, 836

Diagnosis Code Descriptions

Filename: MRKR_ICD_dictionary.csv
Rows: 25,209
Columns: 3

This file contains the description of the ICD9 and ICD10 codes found inMRKR_ICD.csv table.

Field Name	Data Type	Description
ICD9	string	ICD9 code
ICD10	string	ICD10 code
DX_NAME	string	Diagnosis name or description

Data Dictionary v1