Skip to content

covidgraph/data_clinical-trials-gov

 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

86 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Related Article from Kirsten

https://www.s-cubed-global.com/news/covidgraph-nerds-response-to-the-pandemic

Related Issue Tracker

https://github.com/covidgraph/documentation/issues/8

ClinicalTrials.gov Data loader

This python script loads data from ClinicalTrials.gov API into the neo4j based covidgraph. The script gets data from the StudyFields, which are described on this API homepage.

Maintainer: Kirsten

Version: 0.2.1

Neo4j version: < 3.5.17

APOC version: < 3.5.0.11

Docker image location: covidgraph/data-clinical_trials_gov

Usage

Docker

Run prebuild image

docker run -it --rm --name data-cord19 --network host -e NEO4J='{"host":"localhost"}' covidgraph/data-clinical_trials_gov

Build and run local image

docker build -t data-clinical_trials_gov .

docker run -it --rm --name data-cord19 --network host -e NEO4J='{"host":"localhost"}' data-clinical_trials_gov

Envs

The most important Env variables are:

NEO4J: defaults to {"host":"localhost"}. The connections details for the database. For details see https://github.com/covidgraph/motherlode/blob/master/README.md#the-neo4j-connection-string

Python (without Docker)

To run the code without docker you need to have python installed.

Setup

Install the python requirments with

pip install --no-cache-dir -r requirement.txt

Run the script with

python3 ./dataloader/main.py

Data

Queries to ClinicalTrials.gov

Due to a limit of 1000 studies to be returned from a query[https://clinicaltrials.gov/api/gui/demo/simple_study_fields], the queries has been split into 3 parts (syntax for the query): Studies contatining the word COVID for

  1. Obervational studies (COVID AND AREA[StudyType]Observational)
  2. Interventional studies (COVID AND AREA[StudyType]Interventional)
  3. NOT (Observations AND Interventional) studies - e..g expanded access(COVID AND NOT AREA[StudyType]Interventional AND NOT AREA[StudyType]Observational)

Decription of the fields can be found here: https://clinicaltrials.gov/api/gui/ref/crosswalks.

At this point no results information can be found for COVID studies. This will be added once results are avilable.

Scheme

Datascheme

About

Scripts for loading in data from ClinicalTrial.gov

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Languages

  • Python 100.0%