BioGRID-Coronavirus-Biorxiv-Triage

A simple script to take the Biorxiv Coronavirus Collection and Triage it for interaction terms

Requirements

You need to create a new file called config/config.yml containing the settings for your implementation. You can use the config/config.sample.yml file as a template.

Go into the directory containing this repository
Run: pipenv shell
Run: pipenv install
Run: python -m spacy download en_core_web_sm
Create a directory called <DOWNLOAD_PATH> (what you set download_path equal to in the config file)
Run: python run.py -d -e <DATE> where <DATE> is replaced with the date you want to go back to. For example, to fetch papers back to August 15, 2020 use: 2020-08-15
On subsequent runs, if you don't want to re-download the json, you can simply execute: python run.py
Running this script will will create a file called results.csv in the <DOWNLOAD_PATH> folder

Name	Name	Last commit message	Last commit date
Latest commit starkfree Merge pull request #7 from starkfree/master Sep 9, 2020 3f5b587 · Sep 9, 2020 History 20 Commits
config	config	feat: changes source_url in sample config	Aug 26, 2020
.gitignore	.gitignore	feat: first implementation	Apr 2, 2020
LICENSE	LICENSE	Initial commit	Apr 1, 2020
Pipfile	Pipfile	feat: adds config file	Apr 2, 2020
Pipfile.lock	Pipfile.lock	feat: adds config file	Apr 2, 2020
README.md	README.md	doc: updates readme with new run instructions	Sep 9, 2020
config.py	config.py	feat: adds config file	Apr 2, 2020
high_hits.txt	high_hits.txt	feat: adds keywords to keyword lists	May 6, 2020
low_hits.txt	low_hits.txt	feat: first implementation	Apr 2, 2020
med_hits.txt	med_hits.txt	feat: first implementation	Apr 2, 2020
run.py	run.py	fix: fixes code formatting	Sep 9, 2020