inst/QueryLibrary/Aggregate/condition/C10.md

C10: Find an anatomical site by keyword

Description

This query enables a search of all anatomical sites using a keyword entered as input. The resulting concepts could be used in query C11 to identify diseases occurring at a certain anatomical site.

Query

The following is a sample run of the query to list all anatomical site concept IDs specified using a keyword as input.

SELECT
  c.concept_id       AS anatomical_site_id,
  c.concept_name     AS anatomical_site_name,
  c.concept_code     AS anatomical_site_code,
  c.concept_class_id AS anatomical_site_class,
  c.standard_concept AS anatomical_standard_concept,
  c.vocabulary_id    AS anatomical_site_vocab_id
FROM @vocab.concept AS c
WHERE
  lower(c.concept_class_id) = 'body structure' AND
  lower(c.concept_name) LIKE concat('%', lower($1::text), '%') AND
  c.invalid_reason IS NULL
;

Input

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

Output

| Field | Description | | --- | --- | | Anatomical_site_ID | Concept ID of SNOMED-CT anatomical site concept | | Anatomical_site_Name | Name of SNOMED-CT anatomical site concept entered as input | | Anatomical_site_Code | Concept Code of SNOMED-CT anatomical site concept | | Anatomical_site_Class | Concept class of SNOMED-CT anatomical site | | Anatomical_standard_concept | Indicator of standard concept for SNOMED-CT anatomical site | | Anatomical_site_vocab_ID | Vocabulary ID of the vocabulary from which the anatomical site concept is derived from |

Example output record

| Field | Value | | --- | --- | | Anatomical_site_ID | 4103720 | | Anatomical_site_Name | Posterior epiglottis | | Anatomical_site_Code | 2894003 | | Anatomical_site_Class | Body structure | | Anatomical_standard_concept | S | | 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.