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].[Create_Ontology] @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. Create records in the table OntologyUsage in the i2b2ClinDataIntegration database for each study that will use the ontology. The StudyName is the unique portion of the i2b2 database names, for example i2b2_app03_{studyName}_data.
4. Run the command EXECUTE [i2b2ClinDataIntegration].[dbo].[dbo.UpdateOntologyConceptCodesInStudy] @StudyName='GENVASC', @Ontology=##;
   Or update the whole lot however that take around 20 minute, which can be done with EXECUTE [i2b2ClinDataIntegration].[dbo].[UpdateOntologyConceptCodes];

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