Universal vs project-focused
One of the basic first considerations when starting to design an i2b2 project ontology is the primary target audience that is expected to formulate the queries. Basically, there are two types of users:
- people that know the project and therefore know the structure of the data
- people that want to use the data but were not involved in the data collection process
The basic difference between those two groups is that the first one is able to handle labels like "day 14" since they know what to expect under that node. They know which events and visits have been scheduled. They know what data is recorded in "initial visit". Here, one can stick to the original naming. On the contrary, such users would be annoyed by changes that maybe couldn't track, e.g. Items not at the same position where they were on the Case Report Form. This is a case for project-focused navigation ontologies.
Things are different for external researchers or when data from different sources are combined in a research database. Here, an universal ontology has to be created. That means "translating" project-sprecific label into generic ones and moving data. Events can be classified into screening, baseline, intervention, follow-up. Data should be classified into unambiguous groups like demography, diagnosis, laboratory, medications. Whereever possible, mapping data to medical standards or terminologies should be considered.
Depth of the navigation
In most cases, it is adviceable to just stick to the original depth of navigation. But depending on the source format the data came from, this can lead to very deep hierarchies. Examplary for an ODM import, one will find seven levels of hierarchy for a clinical trial: