inspectomop.queries.condition.pathogen_concept_for_keyword

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

Return type:

sqlalchemy.sql.expression.Executable

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;