inst/QueryLibrary/Aggregate/condition/C09.md

In sib-swiss/dsQueryLibraryServer: OMOP query Library

C09: Find all SNOMED-CT condition concepts that can be caused by a given pathogen or causative agent

Description

This query accepts a SNOMED-CT pathogen ID as input and returns all conditions caused by the pathogen or disease causing agent identified using queries C07](http://vocabqueries.omop.org/condition-queries/c7) or [C08.

Query

The following is a sample run of the query to list conditions caused by pathogen or causative agent.

SELECT
  a.concept_id       AS condition_id,
  a.concept_name     AS condition_name,
  a.concept_code     AS condition_code,
  a.concept_class_id AS condition_class,
  a.vocabulary_id    AS condition_vocab_id,
  d.concept_id       AS causative_agent_id,
  d.concept_name     AS causative_agent_name,
  d.concept_code     AS causative_agent_code,
  d.concept_class_id AS causative_agent_class,
  d.vocabulary_id    AS causative_agent_vocab_id
FROM @vocab.concept_relationship AS cr
  JOIN @vocab.concept AS a ON cr.concept_id_1 = a.concept_id
  JOIN @vocab.concept AS d ON cr.concept_id_2 = d.concept_id
WHERE
  cr.relationship_id = 'Has causative agent' AND
  d.concept_id = $1 AND
  cr.invalid_reason IS NULL
;

Input

| Parameter | Example | Mandatory | Notes | | --- | --- | --- | --- | | SNOMED-CT Concept ID | 4248851 | Yes | Concept Identifier for 'Treponema pallidum' |

Output

| Field | Description | | --- | --- | | Condition_ID | Condition concept Identifier | | Condition_Name | Name of the standard condition concept | | Condition_Code | Concept code of the standard concept in the source vocabulary | | Condition_Class | Concept class of standard vocabulary concept | | Condition_Vocab_ID | Vocabulary the standard concept is derived from as vocabulary ID | | Causative_Agent_ID | Pathogen concept ID entered as input | | Causative_Agent_Name | Pathogen Name | | Causative_Agent_Code | Concept Code of pathogen concept | | Causative_Agent_Class | Concept Class of pathogen concept | | Causative_Agent_Vocab_ID | Vocabulary the pathogen concept is derived from as vocabulary ID |

Example output record

| Field | Value | | --- | --- | | Condition_ID | 4326735 | | Condition_Name | Spastic spinal syphilitic paralysis | | Condition_Code | 75299005 | | Condition_Class | Clinical finding | | Condition_Vocab_ID | SNOMED | | Causative_Agent_ID | 4248851 | | Causative_Agent_Name | Treponema pallidum | | Causative_Agent_Code | 72904005 | | Causative_Agent_Class | Organism | | Causative_Agent_Vocab_ID | SNOMED |

Documentation

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

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