r-snippets-bmi

COVID19 Interventional Trials, Observational Studies and Registries

Welcome to the page that collects COVID19 studies registered at ClinicalTrials.gov. This page is updated weekly (each Monday).

Additional important links are

regCOVID

regCOVID stands for REGistered COVID-19 Interventional trials and observational Studies. We chose this acronym/name so that people can refer to the script/project/outputs uniquely.

Report

The report is the most important output. It is linked at the top of this documentation. The link to the report is https://lhncbc.github.io/r-snippets-bmi/regCOVID/regCovid_notebook2.html

Database form of ClinicalTrials.gov data - AACT database

This project relies heavily on prior project by Duke University. It is the AACT database. It stands for Aggregate Analysis of ClinicalTrials.gov. The database offers most recent CTG (=ClinicalTrials.gov) data in database form.

Data lag

AACT database is 48 hours (or so) behind. To eliminate the lag and get more recent data (compared to AACT), you can also use CTG API call like this one: https://clinicaltrials.gov/ct2/results/download_fields?cond=covid-19&down_count=10000&down_flds=all&down_fmt=csv

ClinicalTrials.gov documentation

In addition, data dictionary from CTG is available at https://prsinfo.clinicaltrials.gov/definitions.html and very usefull to researchers extenind this analysis or conducting other CTG based analyses.

Quick Tutorial

For a quick tutorial on how to use the analysis code and data files in this repository go to: https://github.com/lhncbc/r-snippets-bmi/blob/master/regCOVID/regCovid_Tutorial.md

Analysis comments

Search strategies

We use letters to denote search strategies. Strategy A uses title of trial. Strategy B uses free-text condition. Strategy C uses MeSH keywords assigned by CTG (their algorhitm; not publicaly posted).

How to obtain a copy of the database we created

See DESCRIPTION OF EACH DATA FILE. For example, files regCovid_int-a.csv, regCovid_obs-a.csv, and regCovid_reg-a.csv are the lists of interventional trials, observational studies, and registries generated from search method A. Replace letter at the end with b and c to obtain the set of trials using the other search strategy. Note that these files will only include the STUDIES table metadata (from AACT). Inspect the other CSV files that support all the web report analyses to get additional data (e.g., interventions, study updates, etc.)

Code Files

See files with extension .R (regCovid_code_for_analysis.R)
To run the script, you must provide your details for db connection (you must provide your own user name). See their site for instructions https://aact.ctti-clinicaltrials.org/connect.

Code Sections:

Data Files

A list of the data files included and descriptions of what the files are, can be found at this link: https://lhncbc.github.io/r-snippets-bmi/regCOVID/regCOVID_data_file_descript.html

Some file naming conventions we used are:

Feedback

We don’t claim our script is the best approach to analyze certain feature. We are open to suggestions for improvement.

Future additions

References