inspectomop.queries.condition.anatomical_site_by_keyword

inspectomop.queries.condition.anatomical_site_by_keyword(keyword, inspector, return_columns=None)

Retrieves anatomical site concepts given a keyword. Results of this query are useful for condition_concepts_occurring_at_anatomical_site_concept_id

Parameters:

  • keyword (str) – search string. ex ‘Epiglottis’

  • inspector (inspectomop.inspector.Inspector)

  • return_columns (list of str, optional) –

    • optional subset of columns to return from the query

    • columns : [‘concept_id’, ‘concept_name’, ‘concept_code’, ‘concept_class_id’, ‘standard_concept’, ‘vocabulary_id’, ‘vocabulary_name’]

Returns:

results

Return type:

sqlalchemy.sql.expression.Executable

See also

condition_concepts_occurring_at_anatomical_site_concept_id

Notes

Original SQL

C10: Find an anatomical site by keyword:

SELECT
    C.concept_id Anatomical_site_ID,
    C.concept_name Anatomical_site_Name,
    C.concept_code Anatomical_site_Code,
    C.concept_class_id Anatomical_site_Class,
    C.standard_concept Anatomical_standard_concept,
    C.vocabulary_id Anatomical_site_Vocab_ID,
    V.vocabulary_name Anatomical_site_Vocab_Name
FROM
    concept C,
    vocabulary V
WHERE
    LOWER(C.concept_class_id) = 'body structure' AND
    LOWER(C.concept_name) like '%epiglottis%' AND
    C.vocabulary_id = V.vocabulary_id AND
    sysdate BETWEEN C.valid_start_date AND C.valid_end_date;