inspectomop.queries.condition.source_codes_for_concept_ids

inspectomop.queries.condition.source_codes_for_concept_ids(concept_ids, inspector, return_columns=None)

Retreives source condition concepts for OMOP concept_ids. i.e SNOMED-CT –> ICD-9-CM, ICD-10-CM

Parameters:

• source_code (list of int) – integer list of concept_ids to translate

• inspector (inspectomop.inspector.Inspector)

• return_columns (list of str, optional) –

  • optional subset of columns to return from the query

  • columns : [‘concept_id’,’concept_code’, ‘concept_name’, ‘vocab_id’, ‘vocab_name’, ‘domain_id’,’source_concept_id’, ‘source_concept_name’, ‘source_concept_code’, ‘source_concept_class_id’,’source_vocab_id’, ‘source_vocab_name’]

Returns:

results

Return type:

sqlalchemy.sql.expression.Executable

Notes

Original SQL

C06: Translate a given condition to source codes:

set search_path to full_201612_omop_v5;
SELECT DISTINCT
    c1.concept_code,
    c1.concept_name,
    c1.vocabulary_id source_vocabulary_id,
    VS.vocabulary_name source_vocabulary_description,
    C1.domain_id,
    C2.concept_id target_concept_id,
    C2.concept_name target_Concept_Name,
    C2.concept_code target_Concept_Code,
    C2.concept_class_id target_Concept_Class,
    C2.vocabulary_id target_Concept_Vocab_ID,
    VT.vocabulary_name target_Concept_Vocab_Name
FROM
    concept_relationship cr,
    concept c1,
    concept c2,
    vocabulary VS,
    vocabulary VT
WHERE
    cr.concept_id_1 = c1.concept_id AND
    cr.relationship_id = 'Maps to' AND
    cr.concept_id_2 = c2.concept_id AND
    c1.vocabulary_id = VS.vocabulary_id AND
    c1.domain_id = 'Condition' AND
    c2.vocabulary_id = VT.vocabulary_id AND
    c1.concept_id = 312327 AND
    c1.vocabulary_id = 'SNOMED' AND
    sysdate BETWEEN c2.valid_start_date AND c2.valid_end_date;