This project relies on a private cTAKES module for the time being.
Python 2.7 (probably), with the modules listed in
We're using MongoDB to cache trial data locally.
If you want to connect to a SMART container, a SMART 0.6+ container is suggested, though there are hacks to support SMART 0.5.
After initializing the submodules, a symlink to the internally used databases should be functional. If not you must create it:
$ cd clinical-trials-gov $ ln -s ClinicalTrials/databases
There is a SNOMED database at ctakes/ctakes-dictionary-lookup/target/classes/org/apache/ctakes/dictionary/lookup/umls2011ab after checking out cTakes, but it's in HSQLDB format which is not easily usable from Python, so we download and use our own copy:
- download SNOMED CT
from the directory
RF2Release/Full/Terminologyplace the following files under the given name into the
When these files are present, the app will automatically import all SNOMED codes into a local SQLite database, if this has not already been done.
Run the script
ClinicalTrials/databases/rxnorm.sh, it will guide you through installing RxNorm.