inst/QueryLibrary/Aggregate/condition/C11.md

In sib-swiss/dsQueryLibraryServer: OMOP query Library

C11: Find all SNOMED-CT condition concepts that are occurring at an anatomical site

Description

This query accepts a SNOMED-CT body structure ID as input and returns all conditions occurring in the anatomical site, which can be identified using query C10.

Query

The following is a sample run of the query to list conditions located in the anatomical site.

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 anatomical_site_id,
  d.concept_name     AS anatomical_site_name,
  d.concept_code     AS anatomical_site_code,
  d.concept_class_id AS anatomical_site_class,
  d.vocabulary_id    AS anatomical_site_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 finding site' AND
  d.concept_id = $1 AND
  cr.invalid_reason IS NULL
;

Input

| Parameter | Example | Mandatory | Notes | | --- | --- | --- | --- | | SNOMED-CT Concept ID | 4103720 | Yes | Concept Identifier for 'Posterior epiglottis' |

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 | | Anatomical_Site_ID | Body Structure ID entered as input | | Anatomical_Site_Name | Body Structure Name | | Anatomical_Site_Code | Concept Code of the body structure concept | | Anatomical_Site_Class | Concept Class of the body structure concept | | Anatomical_Site_Vocab_ID | Vocabulary the body structure concept is derived from as vocabulary code |

Example output record

| Field | Value | | --- | --- | | Condition_ID | 4054522 | | Condition_Name | Neoplasm of laryngeal surface of epiglottis | | Condition_Code | 126700009 | | Condition_Class | Clinical finding | | Condition_Vocab_ID | SNOMED | | Anatomical_Site_ID | 4103720 | | Anatomical_Site_Name | Posterior epiglottis | | Anatomical_Site_Code | 2894003 | | Anatomical_Site_Class | Body structure | | Anatomical_Site_Vocab_ID | SNOMED |

Documentation

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

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