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: 0.1.1

Neo4j version: < 3.5.17

APOC version: < 3.5.0.11

Docker image location: covidgraph/data-clinical_trials_gov

Usage

Docker

Run

docker run -it --rm --name data-cord19 -e GC_NEO4J_URL="bolt://${HOSTNAME}:7687" covidgraph/data-clinical_trials_gov

Build local image

docker build -t data-clinical_trials_gov .

Run local image

docker run -it --rm --name data-cord19 -e GC_NEO4J_URL='bolt://myneo4jhostname:7687' -e GC_NEO4J_USER=neo4j -e GC_NEO4J_PASSWORD=mysecret data-clinical_trials_gov

Envs

The most important Env variables are:

GC_NEO4J_URL: The full bolt url example 'bolt://myneo4jhostname:7687'

GC_NEO4J_USER: The neo4j user

GC_NEO4J_PASSWORD: The neo4j password

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)

The following study fields are seleted:

NCTId,

StudyType,

Phase,

Condition,

BriefTitle,

LeadSponsorName,

LocationFacility,

LocationCity,

LocationState,

LocationCountry,

InterventionName,

CollaboratorName,

OverallStatus,

PrimaryOutcomeMeasure,

EligibilityCriteria,

StartDate,

StudyFirstSubmitDate,

PrimaryCompletionDate.

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

Example