inspectomop.queries.condition.source_codes_for_concept_ids¶
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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 – a cursor-like object with methods such as fetchone(), fetchmany() etc.
Return type: 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;