inst/QueryLibrary/Aggregate/condition/C08.md

In sib-swiss/dsQueryLibraryServer: OMOP query Library

C08: Find a disease causing agent by keyword

Description

This query enables a search of various agents that can cause disease by keyword as input. Apart from pathogens (see query C07), these agents can be SNOMED-CT concepts of the following classes: - Pharmaceutical / biologic product - Physical object - Special concept - Event - Physical force - Substance

The resulting concepts could be used in query C09 to identify diseases caused by the agent.

Query

The following is a sample run of the query to list all pathogens specified using a keyword as input.

SELECT
  c.concept_id       AS agent_concept_id,
  c.concept_name     AS agent_concept_name,
  c.concept_code     AS agent_concept_code,
  c.concept_class_id AS agent_concept_class,
  c.standard_concept AS agent_standard_concept,
  c.vocabulary_id    AS agent_concept_vocab_id
FROM @vocab.concept AS c
WHERE
  lower(c.concept_class_id) IN ('pharmaceutical / biologic product', 'physical object',
                                'special concept', 'event', 'physical force', 'substance') AND
  lower(c.concept_name) LIKE CONCAT('%', lower($1::text), '%') AND
  c.invalid_reason IS NULL
;

Input

| Parameter | Example | Mandatory | Notes | | --- | --- | --- | --- | | Keyword for pathogen | 'Radiation' | Yes | Keyword without quotes |

Output

| Field | Description | | --- | --- | | Agent_Concept_ID | Concept ID of SNOMED-CT agent concept | | Agent_Concept_Name | Name of SNOMED-CT concept | | Agent_Concept_Code | Concept Code of SNOMED-CT concept | | Agent_Concept_Class | Concept class of SNOMED-CT concept | | Agent_Standard_Concept | Indicator of standard concept for SNOMED-CT concept | | Agent_Vocab_ID | Vocabulary ID of the vocabulary from which the agent concept is derived from (1 for SNOMED-CT) |

Example output record

| Field | Value | | --- | --- | | Agent_Concept_ID | 4220084 | | Agent_Concept_Name | Radiation | | Agent_Concept_Code | 82107009 | | Agent_Concept_Class | Physical force | | Agent_Standard_Concept | S | | Agent_Vocab_ID | SNOMED |

Documentation

https://github.com/OHDSI/CommonDataModel/wiki/concept

sib-swiss/dsQueryLibraryServer documentation built on Feb. 13, 2025, 8:07 p.m.