inspectomop.queries.condition.pathogen_concept_for_keyword¶
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inspectomop.queries.condition.
pathogen_concept_for_keyword
(keyword, inspector, return_columns=None)¶ Retrieves pathogen concepts based on a keyword with ‘Organsim’ as the concept_class_id.
Parameters: - keyword (str) – search string. ex ‘Helicobacter Pylori’
- 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 – a cursor-like object with methods such as fetchone(), fetchmany() etc.
Return type: See also
disease_causing_agents_for_keyword()
,conditions_caused_by_pathogen_or_causative_agent_concept_id()
Notes
Original SQL
C07: Find a pathogen by keyword:
SELECT C.concept_id Pathogen_Concept_ID, C.concept_name Pathogen_Concept_Name, C.concept_code Pathogen_concept_code, C.concept_class_id Pathogen_concept_class, C.standard_concept Pathogen_Standard_Concept, C.vocabulary_id Pathogen_Concept_Vocab_ID, V.vocabulary_name Pathogen_Concept_Vocab_Name FROM concept C, vocabulary V WHERE LOWER(C.concept_class_id) = 'organism' AND LOWER(C.concept_name) like '%trypanosoma%' AND C.vocabulary_id = V.vocabulary_id AND sysdate BETWEEN C.valid_start_date AND C.valid_end_date;