Exploring Concepts with OMOP and SQL

All data collected from participants and health care organizations via surveys, physical measurements, and electronic health records (EHRs) are expressed as “concepts” in OMOP.

Understanding how concepts are defined, organized, and the potential complex relationships that can exist between them in the All of Us dataset will help you decide which concepts to select when you’re building your research cohort.

A benefit of a common data model like OMOP is that the source vocabulary is maintained in the database. When a concept is mapped in OMOP, the source vocabulary is coded as a concept_code.

The concept_code represents the identifier of the concept in the source vocabulary, such as SNOMED-CT, ICD-9, RxNorm, etc. Each concept is also assigned a concept_id which is a unique string of numbers given to a concept.

Because source vocabulary is maintained, you can query data with the source vocabulary or the standard vocabulary. OMOP uses standard vocabulary to map concepts to one another. For a list of the standard vocabulary used by OMOP and an overview of the mapping process, read “Understanding OMOP Basics.”

There are two ways to see if a concept_id is standard or not.

1. Using Athena, a publicly available website maintained by the OMOP community, to browse and explore all the concepts in OMOP.
   
   To identify if a concept is standard or not, you will search by typing into the search bar or by exploring topics by OMOP domain. For example, let’s search for “Type 2 diabetes.”
   
   
   
   The search results display in a list format with multiple columns. The first and second columns are the concept_id and the concept_code followed by the concept_name. The table also includes if the concept is standard or not, which OMOP domain the concept belongs to, and what the standard vocabulary is for the concept.
   
   Using our example, you can see in the Type 2 diabetes search results that the first listing is marked as the standard concept while the second listing is marked as non-standard.
    
2. Querying the concept table and concept relationship table with SQL in the All of Us Researcher Workbench. If the column standard_concept_code is “S” then that concept is standard. If the column is “None,” then that concept is not standard.

Exploring concepts with SQL

Let’s work through an example of pulling data for specific concepts using the programming language SQL.

For this example, we are going to use SQL to build and perform our queries of the OMOP tables. If you do not have SQL experience, you can build your queries using the point-and-click tool Data Explorer.

The standard form of a SQL query includes

SELECT column_name_1, column_name_2, … (You can use * to select all columns from a table)
    FROM table_name
    WHERE condition_to_be_met

Using the standard form of a SQL query, let’s build a query using the example depression with the concept_name, standard concept_id, standard concept_code, or any concept_code.

1. With a concept_name

   Note: Concept_name is not a unique identifier. For example, several concepts are available within the All of Us dataset that describe “depression.” For this example, we will focus on a specific type of depression: major depressive disorder.
   
   SQL Query:

   SELECT *
        FROM concept
        WHERE concept_name = "Major depressive disorder"

   Results:

   concept_id	concept_ name	domain_ id	vocabulary_ id	concept_ class_id	standard_ concept*	concept_ code	valid_ start_ date	valid_ end_ date	invalid_ reason
   1568218	Major depressive disorder, recurrent	Condition	ICD10CM	3-char nonbill code	None	F33	2012-01-01	2099-12-31	None
   4152280	Major depressive disorder	Condition	SNOMED	Clinical Finding	S	370143000	1970-01-01	2099-12-31	None
   44825293	Major depressive disorder, recurrent episode	Condition	ICD9CM	4-dig nonbill code	None	296.3	1970-01-01	2099-12-31	None

   *You can see in this example that we have standard and non-standard concepts from our query in the standard_concept column.

2. With the standard concept_id

   Note: When working with All of Us data, it’s important to work with the standard concept. You can locate the standard concept_id using Athena.
   
   SQL Query:

   SELECT *
        FROM concept
        WHERE concept_id = 4152280

   Results:

   concept_id	concept_name	domain_ id	vocabulary_ id	concept_ class_id	standard_ concept*	concept_ code	valid_ start_ date	valid_ end_ date	invalid_ reason
   4152280	Major depressive disorder	Condition	SNOMED	Clinical Finding	S	370143000	1970-01-01	2099-12-31	None

   *You can see in this example that we used the standard concept_id as denoted by the S in the standard_concept column.
    

3. With the standard concept_code

   Note: When working with All of Us data, it’s important to work with the standard concept. You can locate the standard concept_code using Athena.
   
   SQL Query:

   SELECT *
        FROM concept
        WHERE concept_code = ‘37014300’

   Results:

   concept_id	concept_ name	domain_ id	vocabulary_ id	concept_ class_id	standard_ concept*	concept_ code	valid_ start_ date	valid_ end_ date	invalid_ reason
   4152280	Major depressive disorder	Condition	SNOMED	Clinical Finding	S	370143000	1970-01-01	2099-12-31	None

   *You can see in this example that we used the standard concept_code as denoted by the S in the standard_concept column.
    

4. With the concept_code

   What if you don’t know the concept_name, standard concept_id, or standard concept_code, but you do know the code in another vocabulary (i.e., ICD-9, ICD-10, CPT, etc.)?
   
   Because OMOP retains the source vocabulary, you can search with the code you know. Let’s say you know that major depressive disorder is code 296.30 in ICD-9.
   
   SQL Query:

   SELECT *
        FROM concept
        WHERE concept_code = ‘296.3’

   Results:

   concept_id	concept_ name	domain_ id	vocabulary_ id	concept_ class_id	standard_ concept*	concept_ code	valid_ start_ date	valid_ end_ date	invalid_ reason
   44825293	Major depressive disorder, recurrent episode	Condition	ICD9CM	4-dig nonbill code	None	296.30	1970-01-01	2099-12-31	None

   *You can see in this example that we used the non-standard concept_code as denoted by the None in the standard_concept column.
   
   Let’s say you want to find the standard concept for the non-standard concept. Using the concept_id from the query above, you can find the equivalent standard concept_id with another OMOP table: concept_relationship.
   
   SQL Query:

   SELECT *
        FROM concept_relationship
        WHERE concept_id_1 = 44825293

   Results:

   concept_id_1*	concept_id_2**	relationship_id	valid_start_date	valid_end_date	invalid_reason
   44825293	44829923	Subsumes	2014-10-01	2099-12-31	None
   44825293	44826498	Is a	2014-10-01	2099-12-31	None
   44825293	44831089	Subsumes	2014-10-01	2099-12-31	None
   44825293	44831090	Subsumes	2014-10-01	2099-12-31	None
   44825293	44834589	Subsumes	2014-10-01	2099-12-31	None
   44825293	44827655	Subsumes	2014-10-01	2099-12-31	None
   44825293	4282316	Maps to	2018-02-07	2099-12-31	None
   44825293	44835785	Subsumes	2014-10-01	2099-12-31	None
   44825293	44827656	Subsumes	2014-10-01	2099-12-31	None

   *concept_id_1 is the concept’s source code.
   **concept_id_2 is the concept’s standard code.
   
   The standard concept_id is the string of numbers in the concept_id_2 column of the concept with “Maps to” in the relationship_id column. In the example, 4282316 is the standard concept_id for major depressive disorder.

Exploring concept relationships with SQL

Concepts stored in a common data model like OMOP can have complex relationships. Using the same example as above related to major depressive disorder, we know there are several different types of recurrent major depression, including mild recurrent major depression.

You can explore concepts and their relationships to one another using the concept_relationship table, which we briefly touched on earlier.

Let’s query the concept_relationship table to find concepts that relate to major recurrent depression using the standard concept_id (4282316).

SQL Query:

SELECT *
     FROM concept_relationship
     WHERE concept_id_1 = 4282316

Results:

In the table, you can see all the concepts (concept_id_2) that were mapped to the standard concept for major recurrent depression (concept_id_1 = “4282316”) in the All of Us dataset.

To see additional information about the concepts (concept_id_2), you can join the concept table with the concept_relationship table.

SQL Query:

SELECT cr.relationship_id, c.*
   FROM concept_relationship cr
   JOIN concept c
   ON cr.concept_id_2 = c.concept_id
   WHERE cr.concept_id_1 = 4282316

Results:

Note: This table is only a portion of the resultant table from the SQL query above.

You can see the relationship each concept has in the relationship_id column.

Using the major recurrent depression example, you can see how all the concepts related to major recurrent depression connect together.

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