i2b2 HowTo Create an Ontology

Tags: i2b2 HowTo

Procedure

1. Log into the server UHLSQLBRICCSDB\UHLBRICCSDB and database i2b2ClinDataIntegration
2. Execute the stored procedure [dbo].[CreateEmptyOntology](@OntologyName, @Prefix, @SourceSystem, @OntologyBaseNode, @OntologyDescription)
   • Where:
     • @OntologyName is the name of the ontology and must not contain spaces, e.g., 'EMISPrimaryCareData'
     • @Prefix is the prefix for the concept codes and must not contain spaces, e.g., 'EMISPCD'
     • @SourceSystem is the system from which the data is being copied, e.g., 'Gem Risk Stratification'
     • @OntologyBaseNode is the name of the root node for the ontology, e.g., 'EMISPrimaryCareData'
     • @OntologyDescription is a short description of the ontology, e.g., 'EMIS Primary Care Data from GEM'
3. Execute the stored procedure [dbo].[CreateOntologyInStudy](@OntologyID, @MetaDatabaseName, @DataDatabaseName) for each project that requires the ontology
   • Where:
     • @OntologyID is the ID returned by the previous stored procedure.
     • @MetaDatabaseName is the name of the i2b2 meta database where the ontology should be created, e.g., 'project_MetaData'
     • @DataDatabaseName is the name of the i2b2 data database where the ontology should be created, e.g., 'project_Data'

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