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Playing with the API for ClinicalTrials.gov and LillyCOI
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README.md

ClinicalTrials.gov Eligibility

Extracting and codifying study eligibility criteria from ClinicalTrials.gov using cTakes.

This project relies on a private cTAKES module for the time being.

Requirements

Python

Python 2.7 (probably), with the modules listed in requirements.txt.

MongoDB

We're using MongoDB to cache trial data locally.

SMART Container

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.

Setup

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

SNOMED CT

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/Terminology place the following files under the given name into the databases directory:

    • sct2_Description_Full-en_INT_xxxxxxx.txt: snomed_desc.csv
    • sct2_Relationship_Full_INT_xxxxxxxx.txt: snomed_rel.csv

    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.

RxNorm

Run the script ClinicalTrials/databases/rxnorm.sh, it will guide you through installing RxNorm.

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