Ash: finding the Evil Dead in the scientific literature

There is an urgent need for reviewers and editorial boards to check the reference list of submitted manuscripts, to prevent the spreading of zombie literature. (Bucci 2019)

‘Zombie papers’ just won’t die. (Brainard 2022)

I'm afraid I'm gonna have to ask you to leave the store. (Williams 1992)

Website

I've thrown together www.undead.pub as a basic demo of Ash, so you can get a sense of what we're talking about here.

Python package

Warning

This is a work in progress. The API is subject to change.

Get yourself a copy of the Retraction Watch database, get yourself a paper with some references in it, then try Ash.

First install:

python -m pip install ash-williams

And then something like:

from pprint import pprint

import ash

db = ash.RetractionDatabase("./retractions.csv")
paper = ash.Paper.from_path("./manuscript.docx")
pprint(paper.report(db))

A rudimentary command line interface is currently included for your convenience:

$ ash
Usage: ash [OPTIONS] [PAPER]

  Simple program that runs Ash on PAPER using DATABASE.

Options:
  --database PATH  Path to retractions database file.
  --clear          Clear path to database file.
  --help           Show this message and exit.

$ ash --database ./retractions.csv
Database path: ./retractions.csv

$ ash questionable_paper.docx
Database path: ./retractions.csv
{'dois': {'10.21105/joss.03440': {'Retracted': False}}, 'zombies': []}

The path of the database persists between sessions, so you'll likely need to specify it only the once.

Cloud Notebook

For a full-fledged demonstration without any need to install on your own machine, examine this example notebook through Google Colab.

• Installs Ash in cloud-hosted notebook.
• Provided your email, downloads the Retraction Watch database.
• Runs and reports on a block of text -- or your uploaded file.

Retraction Watch database

Crossref has licensed the Retraction Watch for a five-year term and are making it public including updates, per the official announcement: https://doi.org/10.13003/c23rw1d9. To download the latest data snapshot (~44 MB as of Jul 2024), simply add your email address to the following URL. The csv will automatically download: api.labs.crossref.org/data/retractionwatch?[email protected]

The official home of Retraction Watch appears, at least as of July 2024, to continue to be retractiondatabase.org.