cycquery.mimiciii.MIMICIIIQuerier

class MIMICIIIQuerier(dbms, user='', password='', host='', port=None, database='', schemas=None)

Bases: DatasetQuerier

MIMIC-III dataset querier.

Methods

chartevents	Query MIMICIII chartevents data.
diagnoses	Query MIMICIII diagnosis data.
get_table	Get a table and possibly map columns to have standard names.
labevents	Query MIMICIII labevents data.
list_columns	List columns in a table.
list_custom_tables	List custom tables methods provided by the dataset API.
list_schemas	List schemas in the database to query.
list_tables	List table methods that can be queried using the database.

chartevents()

Query MIMICIII chartevents data.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

diagnoses()

Query MIMICIII diagnosis data.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

get_table(schema_name, table_name, cast_timestamp_cols=True)

Get a table and possibly map columns to have standard names.

Standardizing column names allows for columns to be recognized in downstream processing.

Parameters:

• schema_name (str) – Name of schema in the database.

• table_name (str) – Name of table in the database.

• cast_timestamp_cols (bool) – Whether to cast timestamp columns to datetime.

Returns:

Table with mapped columns.

Return type:

sqlalchemy.sql.selectable.Subquery

labevents()

Query MIMICIII labevents data.

Returns:

Constructed query, wrapped in an interface object.

Return type:

cycquery.interface.QueryInterface

list_columns(schema_name, table_name)

List columns in a table.

Parameters:

• schema_name (str) – Name of schema in the database.

• table_name (str) – Name of table in the database.

Returns:

List of column names.

Return type:

List[str]

list_custom_tables()

List custom tables methods provided by the dataset API.

Returns:

List of custom table names.

Return type:

List[str]

list_schemas()

List schemas in the database to query.

Returns:

List of schema names.

Return type:

List[str]

list_tables(schema_name=None)

List table methods that can be queried using the database.

Parameters:

schema_name (Optional[str]) – Name of schema in the database.

Returns:

List of table names.

Return type:

List[str]