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7-sample-omop-queries.sql
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7-sample-omop-queries.sql
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-- Databricks notebook source
-- MAGIC %md
-- MAGIC You may find this series of notebooks at https://github.com/databricks-industry-solutions/omop-cdm. For more information about this solution accelerator, visit https://www.databricks.com/blog/2021/07/19/unlocking-the-power-of-health-data-with-a-modern-data-lakehouse.html.
-- COMMAND ----------
-- MAGIC %md
-- MAGIC # Example OMOP Queries
-- MAGIC <img src="https://www.ohdsi.org/wp-content/uploads/2015/02/h243-ohdsi-logo-with-text.png" with=150>
-- MAGIC
-- MAGIC In this notebook we share some example queries based on sample queries from https://github.com/OHDSI/OMOP-Queries
-- COMMAND ----------
DESCRIBE DATABASE OMOP531
-- COMMAND ----------
select * from omop531.source_to_standard_vocab_map
-- COMMAND ----------
USE OMOP531
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Find an Observation from a keyword
-- COMMAND ----------
SELECT T.Entity_Concept_Id,
T.Entity_Name,
T.Entity_Code,
T.Entity_Type,
T.Entity_concept_class_id,
T.Entity_vocabulary_id,
T.Entity_vocabulary_name
FROM (
SELECT C.concept_id Entity_Concept_Id,
C.concept_name Entity_Name,
C.concept_code Entity_Code,
'Concept' Entity_Type,
C.concept_class_id Entity_concept_class_id,
C.vocabulary_id Entity_vocabulary_id,
V.vocabulary_name Entity_vocabulary_name,
C.valid_start_date,
C.valid_end_date
FROM concept C,
vocabulary V
WHERE C.vocabulary_id IN ('LOINC', 'UCUM')
AND C.concept_class_id IS NOT NULL
AND C.standard_concept = 'S'
AND C.vocabulary_id = V.vocabulary_id
) T
WHERE locate(LOWER(REPLACE(REPLACE(T.Entity_Name, ' ', ''), '-', '')),
LOWER(REPLACE(REPLACE('LDL' , ' ', ''), '-', ''))) > 0
AND current_date() BETWEEN T.valid_start_date AND T.valid_end_date
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Count of Patients
-- COMMAND ----------
SELECT COUNT(person_id) AS num_persons_count
FROM person
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients of specific gender in the dataset
-- COMMAND ----------
SELECT person.GENDER_CONCEPT_ID, concept.CONCEPT_NAME AS gender_name, COUNT(person.person_ID) AS num_persons_count
FROM person
INNER JOIN concept ON person.GENDER_CONCEPT_ID = concept.CONCEPT_ID
GROUP BY person.GENDER_CONCEPT_ID, concept.CONCEPT_NAME;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients grouped by year of birth
-- COMMAND ----------
SELECT year_of_birth, COUNT(person_id) AS Num_Persons_count
FROM person
GROUP BY year_of_birth
ORDER BY year_of_birth;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients grouped by residence state location
-- COMMAND ----------
SELECT NVL(state, 'XX' )
AS state_abbr, count(*) as Num_Persons_count
FROM person
LEFT OUTER JOIN location
USING( location_id )
GROUP BY NVL( state, 'XX' )
ORDER BY 1;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients grouped by zip code of residence
-- COMMAND ----------
SELECT state, NVL( zip, '9999999' ) AS zip, count(*) Num_Persons_count
FROM person
LEFT OUTER JOIN location
USING( location_id )
GROUP BY state, NVL( zip, '9999999' )
ORDER BY 1, 2;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients by gender, stratified by year of birth
-- COMMAND ----------
SELECT gender_concept_id, c.concept_name AS gender_name, year_of_birth, COUNT(p.person_id) AS num_persons
FROM person p
INNER JOIN concept c ON p.gender_concept_id = c.concept_id
GROUP BY gender_concept_id, c.concept_name, year_of_birth
ORDER BY concept_name, year_of_birth;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## Number of patients by day of the year stratified by day of birth
-- COMMAND ----------
SELECT day_of_birth, COUNT(person_ID) AS num_persons
FROM person
GROUP BY day_of_birth
ORDER BY day_of_birth;
-- COMMAND ----------
SELECT
percentile_25,
median,
percentile_75,
MIN(year_of_birth) AS minimum,
MAX(year_of_birth) AS maximum,
CAST(AVG(year_of_birth) AS INTEGER) AS mean,
STDDEV(year_of_birth) AS stddev
FROM
(
SELECT
MAX(
CASE
WHEN(percentile = 1) THEN year_of_birth
END
) AS percentile_25,
MAX(
CASE
WHEN(percentile = 2) THEN year_of_birth
END
) AS median,
MAX(
CASE
WHEN(percentile = 3) THEN year_of_birth
END
) AS percentile_75
FROM
-- year of birth / percentile
(
SELECT
year_of_birth,
births,
FLOOR(
CAST(
SUM(births) OVER(
ORDER BY
year_of_birth ROWS UNBOUNDED PRECEDING
) AS DECIMAL
) / CAST(
SUM(births) OVER(
ORDER BY
year_of_birth ROWS BETWEEN UNBOUNDED PRECEDING
AND UNBOUNDED FOLLOWING
) AS DECIMAL
)
) + 1 percentile
FROM
-- Year with number of birthsQ
(
SELECT
year_of_birth,
count(*) AS births
FROM
person
GROUP BY
year_of_birth
)
)
where
percentile <= 3
) percentile_table,
person
GROUP BY
percentile_25,
median,
percentile_75;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC # Condition
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C01: Find condition by concept ID
-- MAGIC Find condition by condition ID is the lookup for obtaining condition or disease concept details associated with a concept identifier. This query is a tool for quick reference for the name, class, level and source vocabulary details associated with a concept identifier, either SNOMED-CT clinical finding or MedDRA.
-- COMMAND ----------
SELECT
C.concept_id Condition_concept_id,
C.concept_name Condition_concept_name,
C.concept_code Condition_concept_code,
C.concept_class_id Condition_concept_class,
C.vocabulary_id Condition_concept_vocab_ID,
V.vocabulary_name Condition_concept_vocab_name,
CASE C.vocabulary_id
WHEN 'SNOMED' THEN CASE lower(C.concept_class_id)
WHEN 'clinical finding' THEN 'Yes' ELSE 'No' END
WHEN 'MedDRA' THEN 'Yes'
ELSE 'No'
END Is_Disease_Concept_flag
FROM concept C, vocabulary V
WHERE
C.concept_id = 24134 AND -- Neck Pain
C.vocabulary_id = V.vocabulary_id AND
current_date BETWEEN valid_start_date AND valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C02: Find a condition by keyword
-- MAGIC This query enables search of vocabulary entities by keyword. The query does a search of standard concepts names in the CONDITION domain (SNOMED-CT clinical findings and MedDRA concepts) and their synonyms to return all related concepts.
-- MAGIC
-- MAGIC It does not require prior knowledge of where in the logic of the vocabularies the entity is situated.
-- MAGIC
-- MAGIC The following is a sample run of the query to run a search of the Condition domain for keyword 'myocardial infarction'. The input parameters are highlighted in blue.
-- COMMAND ----------
SELECT
T.Entity_Concept_Id,
T.Entity_Name,
T.Entity_Code,
T.Entity_Type,
T.Entity_concept_class,
T.Entity_vocabulary_id,
T.Entity_vocabulary_name
FROM (
SELECT
C.concept_id Entity_Concept_Id,
C.concept_name Entity_Name,
C.CONCEPT_CODE Entity_Code,
'Concept' Entity_Type,
C.concept_class_id Entity_concept_class,
C.vocabulary_id Entity_vocabulary_id,
V.vocabulary_name Entity_vocabulary_name,
NULL Entity_Mapping_Type,
C.valid_start_date,
C.valid_end_date
FROM concept C
JOIN vocabulary V ON C.vocabulary_id = V.vocabulary_id
LEFT JOIN concept_synonym S ON C.concept_id = S.concept_id
WHERE
(C.vocabulary_id IN ('SNOMED', 'MedDRA') OR LOWER(C.concept_class_id) = 'clinical finding' ) AND
C.concept_class_id IS NOT NULL AND
( LOWER(C.concept_name) like 'myocardial infarction' OR -- e.g. myocardial infarction
LOWER(S.concept_synonym_name) like '%myocardial infarction%' )
) T
WHERE current_date BETWEEN valid_start_date AND valid_end_date
ORDER BY 6,2;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C03: Translate a SNOMED-CT concept into a MedDRA concept
-- MAGIC This query accepts a SNOMED-CT concept ID as input and returns details of the equivalent MedDRA concepts.
-- MAGIC
-- MAGIC The relationships in the vocabulary associate MedDRA 'Preferred Term' to SNOMED-CT 'clinical findings'. The respective hierarchy for MedDRA and SNOMED-CT can be used to traverse up and down the hierarchy of each of these individual vocabularies.
-- MAGIC
-- MAGIC Also, not all SNOMED-CT clinical findings are mapped to a MedDRA concept in the vocabulary.
-- MAGIC
-- MAGIC The following is a sample run of the query to list MedDRA equivalents for SNOMED-CT concept whose concept ID is entered as input.
-- COMMAND ----------
SELECT D.concept_id Snomed_concept_id,
D.concept_name Snomed_concept_name,
D.concept_code Snomed_concept_code,
D.concept_class_id Snomed_concept_class,
CR.relationship_id,
RT.relationship_name,
A.Concept_id MedDRA_concept_id,
A.Concept_name MedDRA_concept_name,
A.Concept_code MedDRA_concept_code,
A.Concept_class_id MedDRA_concept_class
FROM concept_relationship CR, concept A, concept D, relationship RT
WHERE CR.relationship_id = 'SNOMED - MedDRA eq'
AND CR.concept_id_2 = A.concept_id
AND CR.concept_id_1 = 312327
AND CR.concept_id_1 = D.concept_id
AND CR.relationship_id = RT.relationship_id
AND current_date BETWEEN CR.valid_start_date
AND CR.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ##C04: Translate a MedDRA concept into a SNOMED-CT concept
-- MAGIC This query accepts a MedDRA concept ID as input and returns details of the equivalent SNOMED-CT concepts. The existing relationships in the vocabulary associate MedDRA 'Preferred Term' to SNOMED-CT 'clinical findings'. The respective hierarchy for MedDRA and SNOMED-CT can be used to traverse up and down the hierarchy of each of these individual vocabularies.
-- COMMAND ----------
SELECT D.concept_id MedDRA_concept_id,
D.concept_name MedDRA_concept_name,
D.concept_code MedDRA_concept_code,
D.concept_class_id MedDRA_concept_class,
CR.relationship_id,
RT.relationship_name,
A.concept_id Snomed_concept_id,
A.concept_name Snomed_concept_name,
A.concept_code Snomed_concept_code,
A.concept_class_id Snomed_concept_class
FROM concept_relationship CR, concept A, concept D, relationship RT
WHERE CR.relationship_id = 'MedDRA to SNOMED equivalent (OMOP)'
AND CR.concept_id_2 = A.concept_id
AND CR.concept_id_1 = 35205180 --
AND CR.concept_id_1 = D.concept_id
AND CR.relationship_id = RT.relationship_id
AND current_date BETWEEN CR.valid_start_date
AND CR.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C05: Translate a source code to condition concepts
-- MAGIC 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.
-- MAGIC
-- MAGIC Source codes are not unique across different source vocabularies, therefore the source vocabulary ID must also be provided.
-- MAGIC
-- MAGIC The following source vocabularies have condition/disease codes that map to SNOMED-CT concepts:
-- MAGIC
-- MAGIC - ICD-9-CM, Vocabulary_id=2
-- MAGIC - Read, Vocabulary_id=17
-- MAGIC - OXMIS, Vocabulary_id=18
-- MAGIC - ICD-10-CM, Vocabulary_id=34
-- MAGIC
-- MAGIC 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. The sample parameter substitutions are highlighted in blue
-- COMMAND ----------
SELECT DISTINCT
c1.concept_code,
c1.concept_name,
c1.vocabulary_id source_vocabulary_id,
VS.vocabulary_name source_vocabulary_description,
C1.domain_id,
C2.concept_id target_concept_id,
C2.concept_name target_Concept_Name,
C2.concept_code target_Concept_Code,
C2.concept_class_id target_Concept_Class,
C2.vocabulary_id target_Concept_Vocab_ID,
VT.vocabulary_name target_Concept_Vocab_Name
FROM
concept_relationship cr,
concept c1,
concept c2,
vocabulary VS,
vocabulary VT
WHERE
cr.concept_id_1 = c1.concept_id AND
cr.relationship_id = 'Maps to' AND
cr.concept_id_2 = c2.concept_id AND
c1.vocabulary_id = VS.vocabulary_id AND
c1.domain_id = 'Condition' AND
c2.vocabulary_id = VT.vocabulary_id AND
c1.concept_code IN (
'070.0'
) AND c2.vocabulary_id =
'SNOMED'
AND
current_date
BETWEEN c1.valid_start_date AND c1.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C06: Translate a given condition to source codes
-- MAGIC This query allows to search all source codes that are mapped to a SNOMED-CT clinical finding concept. It can be used to translate SNOMED-CT to ICD-9-CM, ICD-10-CM, Read or OXMIS codes.
-- COMMAND ----------
SELECT DISTINCT
c1.concept_code,
c1.concept_name,
c1.vocabulary_id source_vocabulary_id,
VS.vocabulary_name source_vocabulary_description,
C1.domain_id,
C2.concept_id target_concept_id,
C2.concept_name target_Concept_Name,
C2.concept_code target_Concept_Code,
C2.concept_class_id target_Concept_Class,
C2.vocabulary_id target_Concept_Vocab_ID,
VT.vocabulary_name target_Concept_Vocab_Name
FROM
concept_relationship cr,
concept c1,
concept c2,
vocabulary VS,
vocabulary VT
WHERE
cr.concept_id_1 = c1.concept_id AND
cr.relationship_id = 'Maps to' AND
cr.concept_id_2 = c2.concept_id AND
c1.vocabulary_id = VS.vocabulary_id AND
c1.domain_id = 'Condition' AND
c2.vocabulary_id = VT.vocabulary_id AND
c1.concept_id = 312327 --
AND c1.vocabulary_id =
'SNOMED'
AND
current_date
BETWEEN c2.valid_start_date AND c2.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C07: Find a pathogen by keyword
-- MAGIC This query enables a search of all pathogens using a keyword as input. The resulting concepts could be used in query C09 to identify diseases caused by a certain pathogen.
-- COMMAND ----------
SELECT
C.concept_id Pathogen_Concept_ID,
C.concept_name Pathogen_Concept_Name,
C.concept_code Pathogen_concept_code,
C.concept_class_id Pathogen_concept_class,
C.standard_concept Pathogen_Standard_Concept,
C.vocabulary_id Pathogen_Concept_Vocab_ID,
V.vocabulary_name Pathogen_Concept_Vocab_Name
FROM
concept C,
vocabulary V
WHERE
LOWER(C.concept_class_id) = 'organism' AND
LOWER(C.concept_name) like
'%trypanosoma%'
AND C.vocabulary_id = V.vocabulary_id AND
current_date
BETWEEN C.valid_start_date AND C.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C08: Find a disease causing agent by keyword
-- MAGIC This query enables a search of various agents that can cause disease by keyword as input. Apart from pathogens (see query C07), these agents can be SNOMED-CT concepts of the following classes:
-- MAGIC
-- MAGIC Pharmaceutical / biologic product
-- MAGIC Physical object
-- MAGIC Special concept
-- MAGIC Event
-- MAGIC Physical force
-- MAGIC Substance
-- MAGIC The resulting concepts could be used in query C09 to identify diseases caused by the agent.
-- COMMAND ----------
SELECT
C.concept_id Agent_Concept_ID,
C.concept_name Agent_Concept_Name,
C.concept_code Agent_concept_code,
C.concept_class_id Agent_concept_class,
C.standard_concept Agent_Standard_Concept,
C.vocabulary_id Agent_Concept_Vocab_ID,
V.vocabulary_name Agent_Concept_Vocab_Name
FROM
concept C,
vocabulary V
WHERE
LOWER(C.concept_class_id) in ('pharmaceutical / biologic product','physical object',
'special concept','event', 'physical force','substance') AND
LOWER(C.concept_name) like '%cancer%'
AND C.vocabulary_id = V.vocabulary_id AND
current_date
BETWEEN C.valid_start_date AND C.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C09: Find all SNOMED-CT condition concepts that can be caused by a given pathogen or causative agent
-- MAGIC 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 or C08.
-- COMMAND ----------
SELECT
A.concept_Id Condition_ID,
A.concept_Name Condition_name,
A.concept_Code Condition_code,
A.concept_Class_id Condition_class,
A.vocabulary_id Condition_vocab_ID,
VA.vocabulary_name Condition_vocab_name,
D.concept_Id Causative_agent_ID,
D.concept_Name Causative_agent_Name,
D.concept_Code Causative_agent_Code,
D.concept_Class_id Causative_agent_Class,
D.vocabulary_id Causative_agent_vocab_ID,
VS.vocabulary_name Causative_agent_vocab_name
FROM
concept_relationship CR,
concept A,
concept D,
vocabulary VA,
vocabulary VS
WHERE
CR.relationship_ID = 'Has causative agent' AND
CR.concept_id_1 = A.concept_id AND
A.vocabulary_id = VA.vocabulary_id AND
CR.concept_id_2 = D.concept_id AND
D.concept_id = 4248851 -- 4248851
AND D.vocabulary_id = VS.vocabulary_id AND
current_date
BETWEEN CR.valid_start_date AND CR.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C10: Find an anatomical site by keyword
-- MAGIC 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.
-- COMMAND ----------
SELECT
C.concept_id Anatomical_site_ID,
C.concept_name Anatomical_site_Name,
C.concept_code Anatomical_site_Code,
C.concept_class_id Anatomical_site_Class,
C.standard_concept Anatomical_standard_concept,
C.vocabulary_id Anatomical_site_Vocab_ID,
V.vocabulary_name Anatomical_site_Vocab_Name
FROM
concept C,
vocabulary V
WHERE
LOWER(C.concept_class_id) = 'body structure' AND -- body structure
LOWER(C.concept_name) like '%epiglottis%' -- epiglottis
AND C.vocabulary_id = V.vocabulary_id AND
current_date
BETWEEN C.valid_start_date AND C.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC ## C11: Find all SNOMED-CT condition concepts that are occurring at an anatomical site
-- MAGIC 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. Input:
-- COMMAND ----------
SELECT
A.concept_Id Condition_ID,
A.concept_Name Condition_name,
A.concept_Code Condition_code,
A.concept_Class_id Condition_class,
A.vocabulary_id Condition_vocab_ID,
VA.vocabulary_name Condition_vocab_name,
D.concept_Id Anatomical_site_ID,
D.concept_Name Anatomical_site_Name,
D.concept_Code Anatomical_site_Code,
D.concept_Class_id Anatomical_site_Class,
D.vocabulary_id Anatomical_site_vocab_ID,
VS.vocabulary_name Anatomical_site_vocab_name
FROM
concept_relationship CR,
concept A,
concept D,
vocabulary VA,
vocabulary VS
WHERE
CR.relationship_ID = 'Has finding site' AND
CR.concept_id_1 = A.concept_id AND
A.vocabulary_id = VA.vocabulary_id AND
CR.concept_id_2 = D.concept_id AND
D.concept_id = 4103720 --
AND D.vocabulary_id = VS.vocabulary_id AND
current_date BETWEEN CR.valid_start_date AND CR.valid_end_date;
-- COMMAND ----------
-- MAGIC %md
-- MAGIC Copyright / License info of the notebook. Copyright Databricks, Inc. [2021]. The source in this notebook is provided subject to the [Databricks License](https://databricks.com/db-license-source). All included or referenced third party libraries are subject to the licenses set forth below.
-- MAGIC
-- MAGIC |Library Name|Library License|Library License URL|Library Source URL|
-- MAGIC | :-: | :-:| :-: | :-:|
-- MAGIC |Smolder |Apache-2.0 License| https://github.com/databrickslabs/smolder | https://github.com/databrickslabs/smolder/blob/master/LICENSE|
-- MAGIC |Synthea|Apache License 2.0|https://github.com/synthetichealth/synthea/blob/master/LICENSE| https://github.com/synthetichealth/synthea|
-- MAGIC | OHDSI/CommonDataModel| Apache License 2.0 | https://github.com/OHDSI/CommonDataModel/blob/master/LICENSE | https://github.com/OHDSI/CommonDataModel |
-- MAGIC | OHDSI/ETL-Synthea| Apache License 2.0 | https://github.com/OHDSI/ETL-Synthea/blob/master/LICENSE | https://github.com/OHDSI/ETL-Synthea |
-- MAGIC |OHDSI/OMOP-Queries|||https://github.com/OHDSI/OMOP-Queries|
-- MAGIC |The Book of OHDSI | Creative Commons Zero v1.0 Universal license.|https://ohdsi.github.io/TheBookOfOhdsi/index.html#license|https://ohdsi.github.io/TheBookOfOhdsi/|