README.md

Leaf Scripts

Creating Leaf Concepts manually can be done quickly using the Leaf Admin Panel, but certain types of Concepts are best created by SQL script. Here are a few examples of how to do so.

These example assume that you have an active UMLS license and a database named UMLS on the same server as your Leaf application database. Note that ICD10 diagnoses are used just as an example, and you can apply this pattern to ICD9, CPT, LOINC and other coding systems just as easily.

Alternatively, for convenience you can use the scripts in the concepts/ontologies folder to generate the ontologies directly and skip the process of creating temp tables.

ICD10 diagnoses using UMLS

You can find the full example script used here wrapped as a stored procedure at https://github.com/uwrit/leaf-scripts/blob/master/concepts/sp_InsertConceptsFromUMLS.sql.

1. Use the example sp_GetOntologyFromUMLS stored procedure to populate a temporary table (or create the table directly using the ICD10CM.sql script):

CREATE TABLE #Output
(
	AUI NVARCHAR(20) NULL,
	ParentAUI NVARCHAR(20) NULL,
	MinCode NVARCHAR(20) NULL,
	MaxCode NVARCHAR(20) NULL,
	CodeCount INT NULL,
	OntologyType NVARCHAR(20) NULL,
	SqlSetWhere NVARCHAR(1000) NULL,
	UiDisplayName NVARCHAR(1000) NULL
)

INSERT INTO #Output
EXEC dbo.sp_GetConceptOntologyFromUMLS 'ICD10CM'

Output:

AUI	ParentAUI	MinCode	MaxCode	CodeCount	OntologyType	SqlSetWhere	UiDisplayName
A20...	NULL	A00.0	Z99.89	69823	ICD10CM	BETWEEN 'A00.0' AND 'Z99.89'	ICD-10-CM...
A18...	A17...	A02.29	A02.29	1	ICD10CM	= 'A02.29'	Salmonella...
A17...	A174...	A41.81	A41.89	2	ICD10CM	IN ('A41.81','A41.89')	Sepsis...

Each row contains a reference to its parent row via ParentAUI, and a SQL expression in SqlSetWhere which we can plug into our datamodel by prepending our column names.

2. Find the diagnosis SQL Set ID and insert the hierarchical UMLS rows into the app.Concept table:

DECLARE @SqlSetId INT = (SELECT TOP (1) S.Id FROM app.ConceptSqlSet S WHERE S.SqlSetFrom = 'dbo.diagnosis')

INSERT INTO app.Concept
(
   [ExternalId]
  ,[ExternalParentId]
  ,[IsPatientCountAutoCalculated]
  ,[IsNumeric]
  ,[IsParent]
  ,[IsRoot]
  ,[IsSpecializable]
  ,[SqlSetId]
  ,[SqlSetWhere]
  ,[UiDisplayName]
  ,[UiDisplayText]
  ,[AddDateTime]
  ,[ContentLastUpdateDateTime]
)
SELECT 
    [ExternalId]		   = 'UMLS_AUI:' + O.AUI
   ,[ExternalParentId]		   = 'UMLS_AUI:' + O.ParentAUI
   ,[IsPatientCountAutoCalculated] = 1
   ,[IsNumeric]			   = 0		
   ,[IsParent]		           = CASE WHEN EXISTS (SELECT 1 FROM #Output O2 WHERE O.AUI = O2.ParentAUI) THEN 1 ELSE 0 END
   ,[IsRoot]			   = CASE WHEN ParentAUI IS NULL THEN 1 ELSE 0 END
   ,[IsSpecializable]		   = 0
   ,[SqlSetId]			   = @SqlSetId
   ,[SqlSetWhere]		   = '@.CodingSystem = ''ICD10'' AND @.Code ' + O.SqlSetWhere
   ,[UiDisplayName]	           = O.uiDisplayName
   ,[UiDisplayText]		   = 'Had diagnosis of ' + O.UiDisplayName
   ,[AddDateTime]		   = GETDATE()
   ,[ContentLastUpdateDateTime]    = GETDATE()
FROM #Output O
WHERE NOT EXISTS (SELECT 1
		  FROM app.Concept c
		  WHERE 'UMLS_AUI:' + o.AUI = c.ExternalID)

Note that above in

,[SqlSetWhere] = '@.CodingSystem = ''ICD10'' AND @.Code ' + O.SqlSetWhere

The example assumes a hypothetical diagnosis table structure in your clinical database like:

PatientId	CodingSystem	Code	...
A	ICD10	E11.2
B	ICD10	T34.5
C	ICD10	S09.1

Your clinical database columns will likely differ, so tailor this section appropriately for your data.

3. Update the app.Concept.ParentId values using the ExternalId and ExternalParentIds:

UPDATE app.Concept
SET ParentId = p.Id
FROM app.Concept c
	 INNER JOIN (SELECT p.Id, p.ParentId, p.ExternalId
				 FROM app.Concept p) p 
		ON c.ExternalParentID = p.ExternalID
WHERE EXISTS (SELECT 1 FROM #Output o WHERE 'UMLS_AUI:' + o.AUI = c.ExternalId)

And that's it! You'll likely want to have the Leaf Admin Panel open and inspect/tweak these after running the script to make sure everything looks as expected.

You can use this general pattern to insert diagnosis, procedure, LOINC, or other codes.