Publication List with Impact Factor

A python script that fetches all publications of an author from PubMed and adds journal impact factor of the latest Journal Citation Reports (JCR) edition and of the publication year.

Requirements

Python >=3.10 with requests, tqdm, python-dotenv and pandas libraries
Optionally jinja for rendering templates

Installation

Clone or download the repository and install the required libraries using pip:

pip install -r requirements.txt

Clarivate API Key

In order to fetch JCR Impact Factors, you will need an API key from Clarivate Analytics.

Create a file named .env in the same directory as the script and add your Clarivate API key as follows:

CLARIVATE_API_KEY=<your_api_key>

Replace <your_api_key> with your actual Clarivate API key. You can copy the sample.env file in the repository and rename it to .env. Replace the placeholder text in the .env file with your actual API key.

Usage

To run the script, use the following command:

python publication_list.py [-h] \
      -a AUTHORS [AUTHORS ...] \
      -y JCR_YEAR \
      [-o OUTPUT] \
      [--render-template] \
      [--template-filename TEMPLATE_FILENAME] \
      [--template-jif-report {latest,publication_date}] \
      [--summary] \
      [--preprints [PREPRINTS ...]]

Replace <author_name> with the name of the author you want to fetch publications for.

The script will output a CSV file named publications.csv in the current directory. The file will contain amongst others the following columns:

DOI
Authors
Journal Name
Date of Publication
Issue, Volume, Pages
JCR Impact Factor (Latest Edition)
JCR Impact Factor (Publication Year)

Arguments

  -h, --help            show this help message and exit
  -a AUTHORS [AUTHORS ...], --authors AUTHORS [AUTHORS ...]
                        List of author names
  -y JCR_YEAR, --jcr-year JCR_YEAR
                        JCR year to use for JIF (apart from the respective publication years)
  -o OUTPUT, --output OUTPUT
                        Output file name (default: publication-list.csv)
  --render-template     Render a publication list
  --template-filename TEMPLATE_FILENAME
                        Name of template file to render (default: templates/template.tex.jinja2)
  --template-jif-report {latest,publication_date}
                        Which JIF to report in template file (default: latest)
  --summary             Write JIF summary file
  --preprints [DOI ...]
                        List of medRxiv DOIs to include in the publication list

Examples

The following command will fetch publications of Lichtner G and Lichtner Gregor using JIF of 2021 and write the output to custom_output.csv. It will also write LaTeX file and JIF summary file:

python publication_list.py \
  -a "Lichtner G" "Lichtner Gregor" \
  -y "2021" \
  -o "custom_output.csv" \
  --render-template \
  --summary

The following command will fetch publications of Lichtner G using JIF of 2021 and write the output to output/publication-list.csv. It will also render a latex file, output a summary and include preprints from medRxiv:

python publication_list.py \
  -a "Lichtner G" \
  -y 2021 \
  -o "output/publication-list.csv" \
  --render-template \
  --summary \
  --preprints "10.1101/2022.07.18.22277750" "10.1101/2022.05.12.22274089"

Limitations

The JCR Impact Factors are based on the latest edition of the Journal Citation Reports, which is released annually by Clarivate Analytics.
If a publication year or JCR Impact Factor for a specific journal is not available, the corresponding cells in the CSV file will be left blank.

glichtner/publication-list