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https://github.com/crhntr/openfda
A research project studying beta-blockers and adverse events.
https://github.com/crhntr/openfda
Last synced: about 2 months ago
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A research project studying beta-blockers and adverse events.
- Host: GitHub
- URL: https://github.com/crhntr/openfda
- Owner: crhntr
- License: other
- Created: 2017-11-25T22:41:48.000Z (about 7 years ago)
- Default Branch: main
- Last Pushed: 2023-03-06T23:28:17.000Z (almost 2 years ago)
- Last Synced: 2024-06-20T14:18:39.631Z (6 months ago)
- Language: Go
- Homepage:
- Size: 153 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 2
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Metadata Files:
- Readme: ReadMe.md
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README
# openfda
This code is not officially affiliated with the openFDA project.
Right now I am using it for a statistics project and will probably turn it into
a package for studying the various open fda data sets.
Currently the Go structs are not fully compliant with the specification; however,
they have been tested for data/event and work with the majority of records. Not
all special edge cases have been handled.
## Project Navigation
* ./drug - This directory has a go package for manipulating and compressing drug event and label JSON in Go
* ./scripts - has some mongo shell scripts and an R script for data analysis.
* ./www - has a tool for scraping data from the deployed api.fda.org REST api.
* ./ - the root of the package contains standard files (ReadMe.md, .gitignore...) and a compilable cli tool downloading, collecting meta data about, and inserting drug events
## Downloading Data
Note that the data set is huge it is greater than 250 gigs of compressed .json.zip files for the drug event data alone. Plan accordingly.
I used the `unzip` unix tool to decompress the json files.
The json parsing has been somewhat optimized to deal with the huge data (otherwise it would not run on a macbook air with 8gigs of memory).
## Example Research
These data are collected for adverse events (AE) with patients taking beta-blockers, where the beta-blocker is suspected as the cause of the AE. They contain events pulled from 2012q1-2017q3.
```
| total | other | life threatening | hospitalization | disabling | death | congenital anomali |
|--------|-------|-------|------------------|-----------------|-----------|-------|--------------------|
| total | 1794 | 663 | 137 | 798 | 104 | 146 | 7 |
| male | 955 | 283 | 81 | 520 | 48 | 65 | 6 |
| female | 839 | 380 | 56 | 278 | 56 | 81 | 1 |
```