PyMed Wrapper

This script is a wrapper for pymed.

It allows quick batch searching Pubmed and storing results in an Excel sheet.

Installation

pip install -r requirements.txt

Usage

usage: pubmed.py [-h] --tool TOOL --email EMAIL
                 [--author1 AUTHOR1 [AUTHOR1 ...]] [--authors AUTHORS]
                 [--title TITLE [TITLE ...]] [--terms TERMS [TERMS ...]]
                 [--userquery USERQUERY [USERQUERY ...]]
                 [--maxResults MAXRESULTS] [--pubSinceYear PUBSINCEYEAR]
                 [--pubSinceLast PUBSINCELAST]
                 oFile

This script takes in a list of search terms for Pubmed and then uses the pymed
library to connect to the Pubmed API to obtain search results.

positional arguments:
  oFile                 Output file name. Path must exist.

optional arguments:
  -h, --help            show this help message and exit
  --tool TOOL           Your project name. This information is passed onto the
                        Pubmed API.
  --email EMAIL         Your email address. This information is passed onto
                        the Pubmed API.
  --author1 AUTHOR1 [AUTHOR1 ...]
                        First author. Format: Last#First or
                        Last#FirstInitials.
  --authors AUTHORS     Authors. Format: Last#First or Last#FirstInitials.
  --title TITLE [TITLE ...]
                        Title search words.
  --terms TERMS [TERMS ...]
                        List of search terms without Pubmed labels such as
                        [auth] or [ti].
  --userquery USERQUERY [USERQUERY ...]
                        List of search terms that can include Pubmed labels
                        such as [auth] and [ti].
  --maxResults MAXRESULTS
                        Maximum number of results
  --pubSinceYear PUBSINCEYEAR
                        Only results that have been published since <year>.
                        Default=1980
  --pubSinceLast PUBSINCELAST
                        Only results that have been published since the last
                        <x> years (default=not set). This takes precedence
                        over --pubSinceYear.

Examples

./pubmed.py \
    ~/Desktop/myPyMedWrapperTestOutput_Example1.xlsx \
    --tool "myCLIpubmedQuery" \
    --email "my.email@address.com" \
    --terms Alzheimer brain MRI cerebellum \
    --maxResults 200 \
    --pubSinceYear 2010

./pubmed.py \
    ~/Desktop/myPyMedWrapperTestOutput_Example2.xlsx \
    --tool "myCLIpubmedQuery" \
    --email "my.email@address.com" \
    --authors 'Verghese#J Leeuw' \
    --title pain older \
    --maxResults 10 \
    --pubSinceYear 2000

Known Bugs Searching for an author with 'Last Full First Name' (e.g., Doe John) results may not show up. In this case, use 'Last First Initial(s)' (e.g., Doe J).

vnckppl/pymedwrapper

PyMed Wrapper