clinicaltrials Processor (indra_cogex.sources.clinicaltrials)

This module implements input for ClinicalTrials.gov data

NOTE: ClinicalTrials.gov are working on a more modern API that is currently in Beta: https://beta.clinicaltrials.gov/data-about-studies/learn-about-api Once this API is released, we should switch to using it. The instructions for using the current/old API are below.

To obtain the custom download for ingest, do the following

  1. Go to https://clinicaltrials.gov/api/gui/demo/simple_study_fields

  2. Enter the following in the form:

expr= fields=NCTId,BriefTitle,Condition,ConditionMeshTerm,ConditionMeshId,InterventionName,InterventionType,InterventionMeshTerm,InterventionMeshId min_rnk=1 max_rnk=500000 # or any number larger than the current number of studies fmt=csv

  1. Send Request

4. Enter the captcha characters into the text box and then press enter (make sure to use the enter key and not press any buttons).

5. The website will display “please wait… ” for a couple of minutes, finally, the Save to file button will be active.

  1. Click the Save to file button to download the response as a txt file.

7. Rename the txt file to clinical_trials.csv and then compress it as gzip clinical_trials.csv to get clinical_trials.csv.gz, then place this file into <pystow home>/indra/cogex/clinicaltrials/

class ClinicaltrialsProcessor(path=None)[source]

Bases: Processor

get_nodes()[source]

Iterate over the nodes to upload.

get_relations()[source]

Iterate over the relations to upload.