Trial Data / Platform Tour
3. Guided Tour
Which projects are related to head and neck cancer?
- Type “head and neck cancer” into the search bar or go to Human Diseases of the Health Atlas and select “head and neck cancer” in the tree.
- Select the project “LIFE Head and Neck Cancer Group”
- You are now here: https://health-atlas.de/lha/7Q0CR2P3M0-6.
Which trials are available from the LIFE-HNC?
- Scroll down to “Related items”
- Click on “Stratification of head and neck squamous cell carcinomas (HNSCC)” in the “Studies” section; you are now here: https://health-atlas.de/lha/803RKY0RUT-6
Download studie data and metadata of the presented studie
- navigate through the tree by double clicking the data files
- You need user credentials to explore contents from this project (which are: username: lha, password: lha)
- Click on the i2b2 button of one of the data files
- Your are now redirected to the Health Atlas instance of the i2b2 Query and Analysis Tool from the i2b2/tranSMART Foundation (see https://www.i2b2.org/)
- The login form should be pre-filled, if not, use the credentials mentioned above.
- You have now access to all published trial-data of this group.
- In i2b2, look into upper left “Navigate Terms” click on “Trials”. 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 “male” to “Group 1” on the right
- Open “HPV status” and “HPV16 DNA RNA status (code)”; drag “DNA+RNA-” 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”: 16 patients are found. For age distribution scroll “Graph Results” down a little
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:
- http://cri.uchicago.edu/wp-content/uploads/2015/02/i2b2_quick_start_v1.pdf a nice pdf manual
- http://sites.bu.edu/bu-i2b2/intro-to-i2b2/ a nice web intro