Tour 7: Trial Data / Platform tour

Live Demo

Start i2b2

1 Background

Patient-based data from clinical trials cannot generally be made public for data protection reasons. Since there is no concept and few standards for data sharing, a lot of data remains hidden forever.

2 Solution

Data in LHA is systematically prepared together with the data generating groups and then uploaded and presented in various formats and for online exploring. The metadata enriched CDISC ODM format is used consistently, SPSS and Excel formats are generated. The LHA is bound by data protection laws and patient approvals.  Therefore, only basic results of the studies are offered to registered and authorized users online, which is decided by the study management. Metadata is public.

3 Guided Tour

Task: Retreave and view data from Trials of the German High-Grade Non-Hodgkin's Lymphoma Study Group (DSHNHL)

Which project is about non-Hodgkin lymphoma?

Which trials are available from the DSHNHL?

Tools and downloads

Download metadata of the presented dataset:

  • No login/password is required to access metadata
  • Click on “Public Download”/DENSERmetadata.xlsx”
    • Download and open with MS Excel
  • Click in “DENSERodm-metadata.xml” to view metadata in CDISC-ODM format (see https://www.cdisc.org/standards/data-exchange/odm

Download data

  • You need a login/password to access patient related data from this project. E-Mail the "Contact Person" to request an account. (@Reviewer: we are sorry, but you can´t use your login here; our agreement with the studygroup does not cover anonymous access - even for review purposes. You may, however explore the data in i2b2)
  • Click on “Restricted Download/DENSER.CSV” to download Excel compatible data
  • Click on “Restricted Download/DENSER.SAV” to download fully annotated data for IBM SPSS Software
  • Click on “Restricted Download/DENSERodm.XML” to download metadata and clinical data in CDISC-ODM format

Explore Data

  • You need a login/password to explore contents from this project . E-Mail then "Contact Person" to request an account.  (@Reviewer: see your provided login/passwort)
  • Click on "i2b2 Login for DSHNHL required
  • Your are now redirected to the LHA instance of the i2b2 Query and Analysis Tool from the i2b2/tranSMART Foundation  (see https://www.i2b2.org/)
  • Enter login/password; typically the same you used to download of restricted data. If you are registered for more then one group select “DSHNHL”. You have access to all published trial-data of this group:Choose a Projects
  • In i2b2, look into upper left “Navigate Terms” click on “DSHNHL”. This opens all available trial data sets.
    • The number to the right (e.g. 124) indicates how many patients own this “concept”
    • Open “Demography/Sex; drag the concept “female” to “Group 1” on the right
    • Open “EFS-Status”; drag “event” to “Group 2” on the right
    • Click “Run Query”; check “Age patient breakdown” (scroll a little)
    • Click “Ok”; your just performed an sql join statement...
    • See result in in “Graph Results”: 24 patients are found. For age distribution scroll “Graph Results” down a little
i2b2- Query Tool

 

I2b2 queries can be much more complex. A complete introduction to the i2b2 system goes beyond the scope of this tour. Besides the included "Help"-Button on the upper right, there a many public i2b2-manuals available; e.g from Boston University:

Guided Tours

The Core Ontology of Phenotypes

Ontology-Based Specification and Import of Content into the Leipzig Health Atlas

LHA Data Portal

Reference Data for new Phenotypes

Toolbox for Genetic Risk Prediction

Individual Next-Cycle Management for Chemotherapies

OposSOM Browser of B-Cell Lymphoma

GEO-Maps

Trial Data / Platform Tour