Table definitions

Patient info

patient_id_map.csv

Column	Data type	Details
patient_id	str	Original patient ID
deidentified_patient_id	str	deidentified patient ID

patient_dob_map.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
date_of_birth	date	Date of birth of the patient in YYYYMMDD format

Cleaned tables

demographics_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
sex	str	Patient’s sex (gender)
number_of_date_folders	int	Number of unique encounter dates
first_visit_date	datetime	Date of the first recorded medical encounter
last_visit_date	datetime	Date of the last recorded medical encounter
number_of_recorded_admissions	int	Total number of recorded admissions

outpatient_visits_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
department	str	Code representing the department the patient visited
visiting_date	datetime	Date and time when the patient visited the department
unique_record_id	str	Unique identifier for the outpatient visit record

admission_records_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
department	str	Code representing the department where the patient was treated
admission_date	datetime	Date and time of the patient’s admission
time_of_transaction	datetime	The timestamp of the most recent record transaction
time_of_message	datetime	Precise time when the message was generated
unique_record_id	str	Unique identifier for the record

discharge_records_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
discharge_date	datetime	Date and time when the patient was discharged
time_of_transaction	datetime	The timestamp of the most recent record transaction
time_of_message	datetime	Timestamp when the discharge message was generated
discharge_disposition	int	Code representing the patient’s discharge disposition
unique_record_id	str	Unique identifier for the discharge record

diagnosis_records_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
item_code	str	Code representing the diagnosis
item_name	str	Name of the diagnosis
provisional	int	Indicates whether the diagnosis is provisional (1 for true, 0 for false)
diagnosis_type	str	Type of the diagnosis (if available)
time_of_update	datetime	Timestamp when the diagnosis record was last updated
date_of_onset	datetime	Date when the condition or diagnosis started
date_of_diagnosis	datetime	Date when the diagnosis was officially recorded
unique_record_id	str	Unique identifier for the record

prescription_order_records_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
item_code	str	Code representing the prescribed medication
item_name	str	Name of the prescribed medication
duration	str	Duration for which the medication is prescribed
time_of_order	datetime	Timestamp when the prescription was ordered
start_of_order	datetime	Start date and time of the medication prescription
end_of_order	datetime	End date and time of the medication prescription (if available)
unique_record_id	str	Unique identifier for the prescription record

injection_order_records_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
item_code	str	Code representing the medication
item_name	str	Name of the medication
time_of_order	datetime	Timestamp when the medication order was placed
start_of_order	datetime	Start time of the medication order
end_of_order	datetime	End time of the medication order
unique_record_id	str	Unique identifier for the medication order record

laboratory_test_results_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient, including a hospital tag
item_code	str	Code representing the test
item_name	str	Name of the test
numeric	float	Numeric result of the test, if available
nonnumeric	str	Non-numeric result of the test, if available
unit	str	Unit of the numeric test result (e.g., ‘mg/dL’ or ‘no_unit’)
sampled_time	datetime	Timestamp when the specimen was collected
tested_time	datetime	Timestamp when the test was performed
reported_time	datetime	Timestamp when the result was reported
unique_record_id	str	Unique identifier for the record, including a hospital tag

Note

If JLAC10 is not available for item_code, the contents of item_code and item_name are determined using the following rules:

• item_code

  The following items are concatenated with a “|” symbol.

  Example: 001||ER01|0181300_011.

  • The specimen code (from OBR-4)

  • The code for the specimen source (from SPM-8)

  • The code for the laboratory test group (from OBR-4)

  • The raw local laboratory test codes

• item_name

  The following items are concatenated with a “|” symbol.

  Example: “その他||培養同定情報(抗酸菌検査)||Mycobacterium kansasii|同定菌量”.

  • The specimen name (from OBR-4)

  • The name of the specimen source (from SPM-8)

  • The name of the laboratory test group (from OBR-4)

  • The result of the parent laboratory test (from OBR-26; e.g., the bacteria name for the following sensitivity test results)

  • The result of the laboratory test item related to this lab test (e.g., the bacteria name for the following colony size result if the test result is part of a series)

  • The raw local laboratory test name

Maps that need to be prepared by users

Note

• Please prepare the following tables by yourself, and place them in reference_dir. ssmixtools will automatically parse them.

info_atc.csv

Column	Data type	Details
商品名	str	Name of the medication in Japanese
HOT番号	str	The Japanese medication code (HOT code)
YJコード	str	The Japanese medication code (YJ code)
ATC5	str	The medication described in the 5-character ATC code
ATC7	str	The medication described in the 7-character ATC code

Note

• This table is required for ssmixtools.cleaning.mandatory.render_maps().

• Codes not listed in this table will not be automatically mapped to ATC.

ICD10_to_text.csv

Column	Data type	Details
item_code	str	ICD-10 code representing the specific diagnosis
item_name	str	The diagnosis described in English

Note

• This table is needed for ssmixtools.cleaning.optional.step4()

ATC_to_text.csv

Column	Data type	Details
item_code	str	ATC code representing the therapeutic classification and hierarchy
item_name	str	Name or description of the therapeutic category or specific substance

Note

• This table is needed for ssmixtools.cleaning.optional.step4()

Optional maps

optional_text_to_ATC.csv

Column	Data type	Details
text	str	Name of the medication or item in Japanese
counts	int	Number of occurrences or usage of the medication
atc	str	ATC code representing the therapeutic classification of the medication

Note

• Change items in the atc column for mapping.

optional_JLAC10_to_JLAC10.csv

Column	Data type	Details
item_code	str	Code representing the specific laboratory test
item_name	str	Name of the test, including details such as sample type (e.g., ‘LDH_定量値__全血’)
modified	str	Modified or standardized version of the item code, if applicable
listed_by_MEDIS	str	Indicates whether the test is listed by MEDIS (‘Yes’, ‘No’, or ‘Yes (except for method)’)
mean	float	Mean value of the test results
frequent_unit	str	Most frequently used unit for the test results (e.g., ‘U/L’)
numeric_count	int	Number of test results with numeric values
nonnumeric_count	int	Number of test results with non-numeric values
translated	str	Translated description of the test code
comment	str	Additional information or remarks about the test

Note

• Change items in the modified column for mapping. If you want to mark a record as non-test-result (e.g., record just containing supplementary comments), put ‘nar’ (not-a-record) in modified. Or, simply delete the row in this CSV table. Laboratory test records with these marked items will be removed from the dataset and counted.

• method-agnostic form of JLAC10 is allowed in modified. (e.g., 5E0560000001—11)

lab_nonnumerics.csv

Column	Data type	Details
item_code	str	Code representing the laboratory test or item
text	str	Description of the test or analysis, including specimen type and specific test details
nonnumeric	str	Qualitative or categorical result of the test (e.g., ‘(3+)’, ‘(4+)’)
modified	str	Modified version of the nonnumeric result
new_unit	str	Unit of measurement for the test result, or ‘no_unit’ if not applicable
count	int	Frequency or number of occurrences of the result
comment	str	Additional information or remarks about the test result

Note

• Change items in the modified column for mapping.

• If the modified value become numeric value, put its unit in new_unit.

• If you want to mark a record as non-test-result, put ‘nar’ (not-a-record) in modified. Laboratory test records with this nonnumeric result will be removed.

lab_units.csv

Column	Data type	Details
item_code	str	Code representing the specific laboratory test
method_agnostic	str	Code for the test in a method-agnostic format
unit	str	Unit of measurement for the test result (e.g., ‘mg/dL’, ‘no_unit’)
modified	str	Modified or standardized unit of measurement, if applicable
recommended_unit	str	Recommended unit for reporting the test result
add_before_multiplication	float	Constant to add to the result before applying a multiplication factor
multiply_by	float	Factor by which the result is multiplied for normalization or conversion
add_after_multiplication	float	Constant to add to the result after applying the multiplication factor
count	int	Number of occurrences or records for this test result
mean	float	Mean value of the test results
text	str	Description of the test, including specimen type and methodology
comment	str	Additional information or remarks about the test result

Note

• Change items in the modified column for mapping.

• Change constants in add_before_multiplication, multiply_by, and add_after_multiplication if conversion is needed.

• If you want to mark a record as non-test-result, put ‘nar’ (not-a-record) in modified. Laboratory test records with this unit will be removed.

Raw tables

Tables of the extracted clinical records before data cleaning.

patient_metadata_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
sex	str	Patient’s sex (gender)
date_of_birth	datetime	Date of birth
number_of_date_folders	int	Number of unique encounter dates
first_visit_date	datetime	Date of the first recorded medical encounter
last_visit_date	datetime	Date of the last recorded medical encounter
number_of_recorded_admissions	int	Total number of recorded admissions

ADT-12_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
department	str	Name of the clinical department
visiting_date	datetime	Date of outpatient visit

ADT-22_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
department	str	Name of the clinical department
admission_date	datetime	Admission date and time
time_of_transaction	datetime	Timestamp of HL7 message transaction
time_of_message	datetime	Timestamp of HL7 message creation

ADT-52_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
discharge_date	datetime	Discharge date and time
time_of_transaction	datetime	Timestamp of HL7 message transaction
time_of_message	datetime	Timestamp of HL7 message creation
discharge_disposition	str	Disposition of the patient upon discharge

PPR-01_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
primary_diagnosis_coding_system	str	Coding system used for the primary diagnosis
primary_diagnosis_code	str	Code for the primary diagnosis
primary_diagnosis_text	str	Name of the primary diagnosis
secondary_diagnosis_coding_system	str	Coding system used for the backup diagnosis
secondary_diagnosis_code	str	Code for the backup diagnosis
diagnosis_type	str	Type of diagnosis
provisional	int	Flag indicating if the diagnosis is provisional (0 or 1)
time_of_update	datetime	Timestamp of the most recent update in the EHR
date_of_onset	datetime	Date the condition first appeared
date_of_diagnosis	datetime	Date the diagnosis was made

OMP-01_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
primary_prescription_coding_system	str	Coding system used for the primary prescription
primary_prescription_code	str	Code for the primary prescription
primary_prescription_text	str	Name of the primary prescription
secondary_prescription_coding_system	str	Coding system used for the backup prescription
secondary_prescription_code	str	Code for the backup prescription
duration	str	Duration of the prescription (e.g., ‘7 days’)
time_of_order	datetime	Timestamp of when the order was created or updated
start_of_order	datetime	Start time when the order becomes effective
end_of_order	datetime	End time when the order expires

OMP-02_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
injection_type_coding_system	str	Coding system used for the injection type
injection_type_code	str	Code representing the type of injection
injection_type_text	str	Description of the injection type
primary_component_coding_system	str	Coding system used for the primary injection component
primary_component_code	str	Code for the primary injection component
primary_component_text	str	Name of the primary injection component
secondary_component_coding_system	str	Coding system used for the backup injection component
secondary_component_code	str	Code for the backup injection component
time_of_order	datetime	Timestamp of when the order was created or last updated
start_of_order	datetime	Start time when the order becomes effective
end_of_order	datetime	End time when the order expires

OML-11_*.csv

Column	Data type	Details
patient_id	str	Unique identifier for each patient
lab_coding_system	str	Coding system used for the laboratory test
lab_code	str	Code representing the laboratory test
lab_text	str	Name of the laboratory test
value	str	Result value of the laboratory test
unit_text	str	Unit of the test result in text format
unit_code	str	Unit of the test result in coded format
unit_coding_system	str	Coding system used for the unit code
sampled_time	datetime	Time when the specimen was collected
tested_time	datetime	Time when the test was performed
reported_time	datetime	Time when the result was reported