Pubmed Toolkit

A bundle of python scripts searching, downloading pdf, and analyzing from Pubmed.

Installation

Before installation, ensure that you had installed the Python 3 and Pip tool.

1. Clone the repository

git clone https://github.com/kaaass/PubmedToolkit.git
cd PubmedToolkit

2. Install the dependency using pip

pip install -r requirements.txt

pubmed_central.py

Download PDF from pubmed central by PMIDs or PMID Source File. See "PMID Source File Schema" for more detail about the source file schema.

• Support resuming from break point
• Support retrying failed tasks
• Support proxy pool against anti-spider

Usage

usage: pubmed_central.py [-h] [-o OUTPUT_DIR] [--resume] [--retry] [--use-proxy]
                         [PMIDs or PMID source file [PMIDs or PMID source file ...]]

Download PDFs from pubmed central by PMIDs

positional arguments:
  PMIDs or PMID source file
                        PMIDs to download, or filepath of PMID source file.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT_DIR, --output-dir OUTPUT_DIR
                        output directory
  --resume              Allow resume from an exist lock file
  --retry               Retry the tasks in the failed file
  --use-proxy           Use proxy pool to access Pubmed Central

Examples

1. Download pdf from pmid 29138661, 29123944

python pubmed_central.py 29138661 29123944

2. Download pdf from pmid source file

python pubmed_central.py data.json

3. Resume from an interrupted task

python pubmed_central.py data.json

PMID Source File Schema

PMID Source File is a JSON file stores an array of objects. This file could be generated by pubmed_search.py.

[
    {
    	"pmid": 0, // PMID
        // Other attributes will be ignored
	},
    // ...
]

For other formats, you might need to edit the function load_source_file.

Todo

• Support schema: each pmid a line
• Support schema: bibtex library

pubmed_search.py

WARNING: This is an incomplete script, you might need to edit the source code for using it.

Search entries from pubmed using a given query, saving the information as a JSON file.

Usage

Change the variable query to your favor. The query could be built by https://www.ncbi.nlm.nih.gov/pubmed/advanced.

Change the parameter max_results to specify the maximum number of result.

Run python pubmed_search.py, the result will be stored in data.json.

[WIP] pubmed_info.py

Download metadata, figures and extract text from PDFs.

Thanks

1. https://github.com/gijswobben/pymed/
2. https://github.com/zotero/translators