tranSMART tree Hierarchy or Ontology refers to the overall organization and representation of the study concepts in the tranSMART User Interface (UI) as well as to recommended Ontologies and terminology to be used for data curation. eTRIKS project of the European Innovative Medicines Initiative (IMI) has recently released Standards Starter Pack Guidelines for IMI members with recommended Ontologies for data curation and tranSMART Master Tree Hierarchy developed in accordance with CDISC SDTM (Study Data Tabulation Model). Standards Starter Pack can be downloaded using the link on this page in the Resources section (1). SDTM defines a Standard Structure for data to be submitted to the FDA. FDA Janus Clinical Trials Repository (CTR) is built for SDTM formatted data. Maintaining consistent format would greatly facilitate the use of clinical trial data for exploratory research. At the same time, the differences between CTR relational and tranSMART dimensional database model for patient level data has to be taking into consideration for tranSMART tree Hierarchy to maintain data integrity. In tranSMART version 16.2 and earlier all subject level clinical data are loaded into "Oservation Fact" table. Related observations are associated through the category pass.
tranSMART tree Hierarchy is designed as a narrative to Clinical Trial protocol - observations, events and measurements designated as Safety Endpoints are loaded under Clinical Data - Safety Endpoints; assessments, measurements and calculated scores collected and analyzed to assess efficacy are loaded under Clinical Data - Efficacy Endpoints. At the same time, SDTM domains data structure is maintained. Corresponding domain codes are added to the relevant upper level folders (e.g. Adverse Events (AE), Vital Signs (VS),Medical History (MH), etc.). STDM codes are added to Data Labels (e.g. AE by Severity Scale (AESEV), AE by Body System Organ Class (AEBODSYS), etc.) "Narrative" design allows biologists and non-clinical analysts to easily navigate data. SDTM codes can be used to cross-reference tranSMART loaded data with the original data stored in a restricted access clinical trial database. Note that Adverse Events are loaded multiple times to associate each AE "observation fact" with other "observation facts" categorizing Adverse Events.
Observational Study tranSMART tree
Example 23: tranSMART tree for NEPTUNE Study study
Example 2 3 Study curated for loading with tMDataLoader (pre-installed on tranSMART 16.2) can be downloaded using the link on this page in the Resources section (3). NEPTUNE tranSMART tree Ontology file is also attached (4)