This tool is part of my Open Source Clinical Central Monitoring Tool-Set Project.
Clone the repo:
git clone https://github.com/vlshields/NewLineListingValsinstall requirements
pip install -r requirements.txtrun
python new_listing_vals.py- or install the latest release here. Your machine will tell you that it may contain harmful files, this is a false positive. Do not run as administrator!
Sites often enter data in EDC systems later than the respective study documents indicate that they should. This is often refered to as data latency, and it happens at every Clinical Trial. However, some cases are more egregious than others.\ Lets create a mock Phase III clinical trial as an example:
Protocol Title:
A Phase 3, Randomized, Stratified, Observer-Blind,
Placebo-Controlled Study to Evaluate the Efficacy, and Safety of Insomnistop in
Adults with insomnia.
Protocol Number: inso7385
Sponsor Name: Dormira
| Primary endpoints | Clinical Significance Threshold |
|---|---|
| Epworth Sleepiness Score (ESS) | 2 points |
| and Functional Outcomes of Sleep Questionaire | 1 Point |
Theres no mention of specific prohibited medications in the mock protocol, but there are known medications that could effect the studies primary endpoints. Sometimes patients taking such medications should have not met inc/exc in the first place. Other times, the study team my have to render their results unusable.
Lets take Concamitant medications for example. Perhaps a study coordinator neglected to enter a medication in the patients folder, maliciciously or not. Sure DM could have programatic flags for this in EDC,but in a trial with over 1000 patients screened, I think a way to pull automated reports should be available for CMs and DMs.
First lets make some fake data:
# you can modify the fake data however you wish in this file
python fake_listing_data.pyWe pull this first report in november. Take a look at patient 715
We pull another listing in december, take a look at this patient again:
We can see that there were medications entered later for this patient. We would have to go to EDC to look at exactly who, why, and when this data was entered. In a large clinical trial, I tool like this could help us spot these misshaps more quickly.
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Open the program in any directory besides C:\User<yourname>. I suggests making a new folder on your desktop or documents and keeping it there. You can run it the pythonic way or simple click on the .exe file.
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Click and drag your first line listing after prompted. Then drag the listing you want to see changes on.
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THe program should generate an excel file called NewVals{DateofExecustion}.xlsx. Under the indicator columnm, uncheck both to see the old (some become deleted or updated) and new values.
Some data get removed as well:
Make sure to have excel installed or libreoffice installed. I have not tested it in google sheets but if someone does please let me know how it works!
Copyright 2023 Vincent Shields
FPA
- 0.0.1
- Work in progress
