Clinical Data Normalization

Clinical data dictionary

There are two ways to access to clinical data dictionary, where all the clinical meta data is store.

• The google configuration spreadsheet:

https://docs.google.com/spreadsheets/d/1N1p_7fBD6piYKm2C7K7kDkrz-CAfniHZZJGWq_o2bzI/edit#gid=54

The list is under "clinical_attributes" sheet -- by searching keywords and understanding the attributes itself, select the corespondent attribute in the list, and use the ID under "NORMALIZED_COLUMN_HEADER" to replace the original header in the data file. (Notice: this sheet is not up to date, so always confirm with top braid's dictionary).

• Topbraid:

https://evn.mskcc.org/edg/tbl/clinical_data_dictionary.editor

Topbraid is an online platform cbioportal use to manage topology of clinical attributes and meta information. It provides a simple UI. A clinical attribute could be found by either alphabetically in the sublet, or using the search bar at the top left corner.

Adding new attributes

When encounter an attributes that does not exist already in the clinical data dictionary ............