Data from: Making headlines: An analysis of US government-funded cancer research mentioned in online media

This repository provides external input data, code, and analysis scripts to fully reproduce results.

Datasets

Results

The produced dataset consists of 6 different files found in data/results:

• articles_metadata.csv - basic metadata (doi, title, journal, year)
• articles_mesh_term_dummies.csv - dummies for the 13 selected mesh terms
• articles_mesh_subterm_dummies.csv - dummies for 12 mesh subterms
• articles_funding_dummies.csv - dummies for 7 funding types
• articles_news_coverage.csv - news mention counts and dummies for the classified tiers
• news_mentions_details.csv - details about individual news articles (PMID, title, venue_name, venue_url, date, URL, summary, and tier)

Plots

The folder plots contains figures and scripts used to create them.

External datasets

• MeSH terms
  • q2018.bin - (available at the NIH FTP server here)
  • d2018.bin - (available at the NIH FTP server here)
• List of news outlets (provided by Altmetric.com)

Reproduce results

1. Clone the repository including submodules git clone git@github.com:ScholCommLab/cancer-news.git

2. Install requirements

   • Python pip install -r requirements.txt
   • R
     • rentrez
     • jsonlite

3. Copy example_config.yml to config.yml and insert your Altmetric key.

4. Run the following scripts:

   1. Collect PubMed data Rscript 01_collect_pubmed.R

   2. Collect altmetrics from Altmetric.com python 02_collect_altmetrics.py

   3. Create dummy variables and export data python 03_export_data.py

License

The created dataset, as specified in the description of results, is published in the public domain. No rights reserved.

External datasets

Data provided by the National Library of Medicine (NLM) is distributed under the same conditions as specified by the NLM: https://www.nlm.nih.gov/databases/download/terms_and_conditions.html

Data provided by Altmetric.com LLC cannot be further redistributed without their permission.