= 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=##;`[[BR]] Or update the whole lot however that take around 20 minute, which can be done with `EXECUTE [i2b2ClinDataIntegration].[dbo].[UpdateOntologyConceptCodes];`


[[BackLinks]]