inspectomop.queries.condition.condition_concepts_for_source_codes

inspectomop.queries.condition.condition_concepts_for_source_codes(source_codes, inspector, return_columns=None)

Retrieves standard condition concepts for source codes. Ex ICD-9-CM –> SNOMED-CT

Parameters:

• source_codes (list of str) – a list of source code strings. Ex ICD-9-CM [‘250.00’,‘250.01’]
• inspector (inspectomop.inspector.Inspector) –
• return_columns (list of str, optional) –
  • optional subset of columns to return from the query
  • columns : [‘source_code’, ‘source_concept_name’, ‘source_vocab_id’, ‘source_vocab_name’, ‘source_domain_id’,’target_concept_id’, ‘target_concept_name’, ‘target_concept_code’, ‘target_concept_class_id’,’target_vocab_id’, ‘target_vocab_name’]

Returns:

results – a cursor-like object with methods such as fetchone(), fetchmany() etc.

Return type:

inspectomop.results.Results

Notes

Original SQL

C05: Translate a source code to condition concepts:

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_code IN ('070.0') AND
    c2.vocabulary_id ='SNOMED' AND
    sysdate BETWEEN c1.valid_start_date AND c1.valid_end_date;