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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. 

Original data structure, user group, planned data use and tranSMART database architecture are the four main factors to consider when designing a master tranSMART tree for a project. The intend of this Library is to collect examples of different tranSMART trees used by the Community.

Clinical Trial tranSMART tree

Clinical trial data combined with genetic or high dimensional exploratory biomarkers can provide a treasure trove of data for exploratory research. tranSMART tree Hierarchy design can facilitate navigation and interpretation of different observations, events, measurements, safety and efficacy assessments and other patient level data collected in the course of a clinical trial.

Example 1: tranSMART tree fin SDTM Format:


Example 2: tranSMART tree for Parallel Design Clinical Trial:


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.

Example 2 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 (2).

Observational Study tranSMART tree

Example 3: tranSMART tree for NEPTUNE Study study

 

Example 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)

Resources

 

  1. eTRIKS-Standards-Starter-Pack-v1.0.pdf
  2. Rheumatoid Arthritis_STUDYABC_NewDrugABC Phase 2.zip
  3. NEPT-TEST.zip
  4. NEPTUNE_tranSMART_v1_4_Ontology.xlsx
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