API Reference

Inspector

inspectomop.Inspector

Constructor

Inspector(connection_url)

Creates an Inspector object which can be used to run OMOP data queries

Attributes

Inspector.connection_url	password@host:port/database' used to specify the dialect, location, etc.
Inspector.engine	A convenience hook to the underlying sqlalchemy engine.
Inspector.tables	A dictionary containing all OMOP CDM tables in the connected database.
Inspector.vocabularies_tables	A dictionary containing all of the Vocabularies OMOP CDM tables in the connected database.
Inspector.metadata_tables	A dictionary containing all of the MetaData OMOP CDM tables in the connected database.
Inspector.clinical_tables	A dictionary containing all of the Clinical OMOP CDM tables in the connected database.
Inspector.health_system_tables	A dictionary containing all of the Health System OMOP CDM tables in the connected database.
Inspector.health_economics_tables	A dictionary containing all of the Health Economics OMOP CDM tables in the connected database.
Inspector.derived_elements_tables	A dictionary containing all of the Derived Elements OMOP CDM tables in the connected database.

Methods

Inspector.attach_sqlite_db(db_file, schema_name)	For SQLite backends, attaches an additional sqlite database file.
Inspector.connect()	Provides a Connection to the underlying database from the connection pool.
Inspector.table_info(table_name)	Return a Pandas DataFrame describing the fields and properties of a table.

Connection

inspectomop.Connection

Constructor

Connection(engine[, connection, ...])

A subclass of sqlalchemy.engine.Connection.

Warning

Although a public constructor exists, Connection objects are meant to be instantiated indirectly from calls to Inspector.connect()

Methods

Connection.execute(statement[, parameters, ...])

Executes an SQL query on the OMOP CDM.

Results

inspectomop.Results

Constructor

Results(cursor_result)

A cursor-like object with methods such as fetchone, fetchmany etc.

Warning

Although a public constructor exists, Results objects are meant to be instantiated indirectly from calls to Connection.execute()

Methods

Results.as_pandas()	Return all rows from a results object as a pandas DataFrame
Results.as_pandas_chunks(chunksize)	Yields a pandas DataFrame with n_rows = chunksize

Queries

inspectomop.queries

Care Site

inspectomop.queries.care_site

facility_counts_by_type(inspector[, ...])	Returns facility counts by type in the OMOP CDM i.e. # Inpatient Hospitals, Offices, etc.
patient_counts_by_care_site_type(inspector)	Returns patients counts by facility type.

Condition

inspectomop.queries.condition

anatomical_site_by_keyword(keyword, inspector)	Retrieves anatomical site concepts given a keyword.
condition_concept_for_concept_id(concept_id, ...)	Retrieves the condition concept for a condition_concept_id.
condition_concepts_for_keyword(keyword, ...)	Retrieves standard concepts for a condition/keyword.
condition_concepts_for_source_codes(...[, ...])	Retrieves standard condition concepts for source codes.
condition_concepts_occurring_at_anatomical_site_concept_id(...)	Retrieves condition concepts that occur at a given anatomical site.
conditions_caused_by_pathogen_or_causative_agent_concept_id(...)	Retreives all conditions caused by a pathogen or other causative agent concept_id.
disease_causing_agents_for_keyword(keyword, ...)	Retrieves disease causing agents by keyword.
source_codes_for_concept_ids(concept_ids, ...)	Retreives source condition concepts for OMOP concept_ids.
pathogen_concept_for_keyword(keyword, inspector)	Retrieves pathogen concepts based on a keyword with 'Organsim' as the concept_class_id.
place_of_service_counts_for_condition_concept_id(...)	Provides counts of conditions stratified by place_of_service (Office, Inpatient Hospital, etc.)

Drug

inspectomop.queries.drug

drug_classes_for_drug_concept_id(concept_id, ...)	Returns drug classes for drug or ingredient concept_ids.
drug_concepts_for_ingredient_concept_id(...)	Get all drugs that contain a given ingredient.
indications_for_drug_concept_id(concept_id, ...)	Find all indications for a drug given a concept_id.
ingredients_for_drug_concept_ids(...[, ...])	Get ingredients for brand or generic drug concept_ids.
ingredient_concept_ids_for_ingredient_names(...)	Get concept_ids for a list of ingredients.

General

inspectomop.queries.general

ancestors_for_concept_id(concept_id, inspector)	Find all ancestor concepts for a concept_id.
children_for_concept_id(concept_id, inspector)	Find all child concepts for a concept_id.
concepts_for_concept_ids(concept_ids, inspector)	Returns concept information for a list of concept_ids
descendants_for_concept_id(concept_id, inspector)	Find all descendant concepts for a concept_id.
parents_for_concept_id(concept_id, inspector)	Find all parent concepts for a concept_id.
related_concepts_for_concept_id(concept_id, ...)	Find all concepts related to a concept_id.
siblings_for_concept_id(concept_id, inspector)	Find all sibling concepts for a concept_id i.e.(concepts that share common parents).
synonyms_for_concept_ids(concept_ids, inspector)	Returns concept information for a list of concept_ids
standard_vocab_for_source_code(source_code, ...)	Convert source code to all mapped standard vocabulary concepts.

Observation

inspectomop.queries.observation

observation_concepts_for_keyword(keyword, ...)

Search for LOINC and UCUM concepts by keyword.

Payer Plan

inspectomop.queries.payer_plan

counts_by_years_of_coverage(inspector)	Returns counts of payer coverage based on continuous coverage (payer_plan_period_start_date - payer_plan_period_end_date)365.25.
patient_distribution_by_plan_type(inspector)	Returns counts of payer coverage by plan type.

Person

inspectomop.queries.person

patient_counts_by_gender(inspector[, ...])	Returns patient counts grouped by gender for the database or alternativily, for a supplied list of person_ids.
patient_counts_by_year_of_birth(inspector[, ...])	Returns patient counts grouped by year of birth for the database or alternativily, for a supplied list of person_ids.
patient_counts_by_residence_state(inspector)	Returns patient counts grouped by state for the database or alternativily, for a supplied list of person_ids.
patient_counts_by_zip_code(inspector[, ...])	Returns patient counts grouped by zip code for the database or alternativily, for a supplied list of person_ids.
patient_counts_by_year_of_birth_and_gender(...)	Returns patient counts stratified by year of birth and gender for the database or alternativily, for a supplied list of person_ids.