inst/QueryLibrary/Aggregate/condition/C05.md

In sib-swiss/dsQueryLibraryServer: OMOP query Library

C05: Translate a source code to condition concepts

Description

This query enables to search all Standard SNOMED-CT concepts that are mapped to a condition (disease) source code. It can be used to translate e.g. ICD-9-CM, ICD-10-CM or Read codes to SNOMED-CT.

Source codes are not unique across different source vocabularies, therefore the source vocabulary ID must also be provided.

The following source vocabularies have condition/disease codes that map to SNOMED-CT concepts:

• ICD-9-CM
• Read
• OXMIS
• ICD-10-CM

Query

The following is a sample run of the query to list SNOMED-CT concepts that a set of mapped codes entered as input map to.

SELECT DISTINCT
  c1.concept_code     AS source_code,
  c1.concept_name     AS source_name,
  c1.vocabulary_id    AS source_vocabulary_id,
  c2.concept_id       AS target_concept_id,
  c2.concept_name     AS target_concept_name,
  c2.concept_code     AS target_concept_code,
  c2.concept_class_id AS target_concept_class,
  c2.vocabulary_id    AS target_concept_vocab_id
FROM @vocab.concept_relationship AS cr
  JOIN @vocab.concept AS c1 ON cr.concept_id_1 = c1.concept_id
  JOIN @vocab.concept AS c2 ON cr.concept_id_2 = c2.concept_id
WHERE
  cr.relationship_id = 'Maps to' AND
  c1.concept_code = $1::text AND
  c1.vocabulary_id = $2::text AND
  c1.invalid_reason IS NULL
;

Input

| Parameter | Example | Mandatory | Notes | | --- | --- | --- | --- | | Source Code List | '070.0' | Yes | Source codes are alphanumeric and need to be entered as a string without quotes. | | Source Vocabulary ID | 'ICD9CM' | Yes | The source vocabulary is mandatory, because the source ID is not unique across different vocabularies. |

Output

| Field | Description | | --- | --- | | Source_Code | Source code for the disease entered as input | | Source_Code_Description | Description of the source code entered as input | | Source_Vocabulary_ID | Vocabulary the disease source code is derived from as vocabulary ID | | Source_Domain_ID | Type of mapping or mapping domain, from source code to target concept. Example Condition, Procedure, Drug etc. | | Target_Concept_ID | Concept ID of the target condition concept mapped to the disease source code | | Target_Concept_Name | Name of the target condition concept mapped to the disease source code | | Target_Concept_Code | Concept code of the target condition concept mapped to the disease source code | | Target_Concept_Class | Concept class of the target condition concept mapped to the disease source code | | Target_Concept_Vocab_ID | Vocabulary the target condition concept is derived from as vocabulary code |

Example output record

| Field | Value | | --- | --- | | Source_Code | 070.0 | | Source_Code_Description | Viral hepatitis | | Source_Vocabulary_ID | ICD9CM | | Source_Domain_ID | CONDITION | | Target_Concept_ID | 4291005 | | Target_Concept_Name | VH - Viral hepatitis | | Target_Concept_Code | 3738000 | | Target_Concept_Class | Clinical finding | | Target_Concept_Vocab_ID | SNOMED |

Documentation

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

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