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.
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
;
| Parameter | Example | Mandatory | Notes | | --- | --- | --- | --- | | Keyword for pathogen | 'Epiglottis' | Yes | Keyword without quotes|
| 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 |
| 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 |
https://github.com/OHDSI/CommonDataModel/wiki/
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