pubSight: creating a summary figure of PUBMED publications direction

pubSight , a visualization tools.

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Citation:

Mahdi Baghbanzadeh, Bahar Sayoldin, Ali Rahnavard (2023+). pubSight: creating a summary figure of publications in PUBMED database for literature direction, https://github.com/omicsEye/pubSight/.

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pubSight user manual

Contents

• pubSight
• Installation
• Getting Started with pubSight
• Examples
• Support

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pubSight

pubSight is a Python package that visualizes the number of publications in specific fields using PubMed records. It allows users to input a list of queries and make API calls to PubMed with Entrez to retrieve data. The retrieved data is then processed and visualized using Matplotlib.

Installation

• First install conda
  Go to the Anaconda website and download the latest version for your operating system.
• For Windows users: do not forget to add conda to your system path
• Second is to check for conda availability
  open a terminal (or command line for Windows users) and run:

conda --version

it should out put something like:

conda 4.9.2

if not, you must make conda available to your system for further steps. if you have problems adding conda to PATH, you can find instructions here.

install git

1. Create a new conda environment (let's call it pubSight_env) with the following command:

conda create --name pubSight_env python=3.9

2. Activate your conda environment:

conda activate pubSight_env 

3. Install pubSight: install with pip (NOT AVAILABLE NOW, please use the next option):

pip install pubSight

or you can directly install if from GitHub:

python -m pip install git+https://github.com/omicsEye/pubSight

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Getting Started with pubSight

You can use pubSight in a Python IDE or through the command line. The following are the available command line arguments:

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT, -i INPUT
                        path to file that has all the query terms
  --email EMAIL, -e EMAIL
                        a valid email address
  --out_dir OUT_DIR, -o OUT_DIR
                        path to report directory
  --color_palette COLOR_PALETTE, -c COLOR_PALETTE
                        Matplotlib color palette
  --group_legend, -g   make a group legend for the whole plot
  --pubmed_data PUBMED_DATA, -p PUBMED_DATA
                        path to a CSV dataframe that has four columns ['year', 'count', 'main_term', 'sub_term']

Here's an example usage:

pubSight --input queries.txt --email example@example.com --out_dir report --color_palette viridis --group_legend

This command retrieves data from PubMed based on the queries listed in the file queries.txt. It uses the email address example@example.com for Entrez, saves the report to the directory report, uses the color palette viridis, and creates a group legend for the whole plot.

Examples

Here are some examples of visualizations created using pubSight:

Support

• Please submit your questions or issues with the software at Issues tracker.