omop.OMOP_match

source

OMOPMatcher

class OMOPMatcher(
	logger: Logger
)

This class retrieves matches from an OMOP database and returns the best

Methods

__init__

def __init__(
	logger: Logger
)

close

def close()

Close the engine connection.

calculate_best_matches

def calculate_best_matches(
	search_terms: str[List]
	vocabulary_id: 
	concept_ancestor: bool
	concept_relationship: bool
	concept_synonym: bool
	search_threshold: int
	max_separation_descendant: int
	max_separation_ancestor: int
)

Calculate best OMOP matches for given search terms

Calls fetch_OMOP_concepts on every item in search_terms.

Parameters

search_terms: List[str] A list of queries to send to the OMOP database

vocabulary_id: str An OMOP vocabulary_id to pass to the OMOP query to restrict the concepts received to a specific vocabulary

concept_ancestor: bool If true, then calls fetch_concept_ancestor()

concept_relationship: bool If true, then calls fetch_concept_relationship()

concept_synonym: bool If true, then queries the synonym table of the OMOP database for matches to the search terms

search_threshold: int The threshold on fuzzy string matching for returned results

max_separation_descendant: int The maximum separation to search for concept descendants

max_separation_ancestor: int The maximum separation to search for concept ancestors

Returns

list A list of results for the search terms run with the other parameters provided.

fetch_OMOP_concepts

def fetch_OMOP_concepts(
	search_term: str
	vocabulary_id: 
	concept_ancestor: bool
	concept_relationship: bool
	concept_synonym: bool
	search_threshold: int
	max_separation_descendant: int
	max_separation_ancestor: int
)

Fetch OMOP concepts for a given search term

Runs queries against the OMOP database If concept_synonym is false, then a query is run that queries the concept table alone. If concept_synonym is true, then this search is expanded to the concept_synonym table.

Any concepts returned by the query are then filtered by fuzzy string matching. Any concepts satisfying the concept threshold are returned.

If the concept_ancestor and concept_relationship arguments are true, the relevant methods are called on these concepts and the result added to the output.

Parameters

search_term: str A search term for a concept inserted into a query to the OMOP database

vocabulary_id: list[str] A list of OMOP vocabularies to filter the findings by

concept_ancestor: str If true then appends the results of a call to fetch_concept_ancestor to the output

concept_relationship: str If true then appends the result of a call to fetch_concept_relationship to the output

concept_synonym: str If true, checks the concept_synonym table for the search term

search_threshold: int The threshold on fuzzy string matching for returned results

max_separation_descendant: int The maximum separation to search for concept descendants

max_separation_ancestor: int The maximum separation to search for concept ancestors

Returns

list | None A list of search results from the OMOP database if the query comes back with results, otherwise returns None

fetch_concept_ancestor

def fetch_concept_ancestor(
	concept_id: str
	max_separation_descendant: int
	max_separation_ancestor: int
)

Fetch concept ancestor for a given concept_id

Queries the OMOP database’s ancestor table to find ancestors for the concept_id provided within the constraints of the degrees of separation provided.

Parameters

concept_id: str The concept_id used to find ancestors

max_separation_descendant: int The maximum level of separation allowed between descendant concepts and the provided concept

max_separation_ancestor: int The maximum level of separation allowed between ancestor concepts and the provided concept

Returns

list A list of retrieved concepts and their relationships to the provided concept_id

fetch_concept_relationship

def fetch_concept_relationship(
	concept_id: 
)

Fetch concept relationship for a given concept_id

Queries the concept_relationship table of the OMOP database to find the relationship between concepts

Parameters

concept_id: str An id for a concept provided to the query for finding concept relationships

Returns

list A list of related concepts from the OMOP database

run

def run(
	search_term: list[str]
	logger: Logger
	vocabulary_id: list[str]
	search_threshold: int
	concept_ancestor: bool
	concept_relationship: bool
	concept_synonym: bool
	max_separation_descendant: int
	max_separation_ancestor: int
)

Runs queries against the OMOP database

Loads the query options from BaseOptions, then uses these to select which queries to run.

Parameters

vocabulary_id: list[str] A list of vocabularies to use for search

concept_ancestor: bool Whether to return ancestor concepts in the result

concept_relationship: bool Whether to return related concepts in the result

concept_synonym: bool Whether to explore concept synonyms in the result

search_threshold: int The fuzzy match threshold for results

max_separation_descendant: int The maximum separation between a base concept and its descendants

max_separation_ancestor: int The maximum separation between a base concept and its ancestors

search_term: str The name of a drug to use in queries to the OMOP database

logger: Logger A logger for logging runs of the tool

Returns

list A list of OMOP concepts relating to the search term and relevant information