Motivation

With the Mapping Editor advanced i2b2 ontologies can be created with specific end-users in mind. The editor consists of three areas: at the top are options for saving, loading und upload of ontologies. The bottom consists of two windows the source ontology (left) and target ontology (right).

The source ontology represents an i2b2 project which was filled with data with the import browser. The target ontology represents a user defined advanced i2b2 project which was created using data from the source ontology. The source ontology is not editable; it is only defined by loading data into the i2b2 project via the Import Browser. After creating a target ontology, this new i2b2 ontology with its corresponding patient data will be uploaded to an i2b2 project chosen by the user. 

Loading, saving and uploading of i2b2 ontologies

A source ontology can be loaded into the Mapping Editor by right-clicking an i2b2 project in the Import Browser and selecting "Load Ontology" or by simply dragging an i2b2 project onto the Mapping Editor. If it is the first time this i2b2 project is loaded in the Mapping Editor, a new and empty target ontology is created and three tables in database will be created which store data needed by the Mapping Editor. If a target ontology was already created, it will be automatically loaded and work can resume. The user created target ontology can be stored by clicking the floppy disc button. Target ontologies can also by versioned by clicking the plus button. Old version can be loaded by the adjunct drop down menu and deleted with the red cross. Since the editor does not support an undo function it is recommend to use the versioning when extensively editing a project. You can give the target ontology a name and a description by clicking the "edit" button on the left of the versioning options.

To define an i2b2 project in which the target ontology should be uploaded, drag an i2b2 project from the Import Browser onto the "Target Project" field in the Mappping Editor. After clicking the "Upload" button, the target ontology will be uploaded in the i2b2, concept and modifier_dimension of the target i2b2 project. All patient data from the source i2b2 project will be modified according to the transformation rules defined when creating the target ontology. This patient data will also be uploaded to the observation_fact and the patient related tables of the target i2b2 project and can then be queried with any i2b2 query tool.