paperchaser

A script that accepts a file of author names and prints out the collective papers of these authors. No duplicaitons, i.e. of two or more authors collaborated on a paper, that paper will appear only once. The script uses Biopython's Entrez utilities to get the papers from the PubMed database. Other manuscript repositories are not supported currently.

Prerequisites

Python >3.6
Biopython https://biopython.org

Installation

Download paperchaser

Running

Example. Note that this example will not run unless you replace the --email argument with a valid email address.

python paperchaser -n "Iddo Friedberg" --email="your_email_here" --years 2015 2021 --outfile="my_refs.txt" --affil="Iowa State University"

Arguments

-n, --names list of authors, comma delimieted, blank separated. Example: -n "Joe Smith" "Jane Doe"
-i, --infile if more than one author, it is preferable to read them in from a file.
-m, --email user email. Required by NCBI and therefore required. The author of this software couldn't care less about your email address.
-y, --years year range. E.g. --years 2007 2020 will filter by papers published only between 2007 and 2020, inclusive. Default: 1930 until one year after the current year.
-o, --outfile output file. Optional. Default: screen output.
-s, --datesort {f,F,r,R,forward,reverse} sort by date, [f]orward or [r]everse. Default: forward
-a, --affil Institutional affiliation. Optional, but highly recommended if this script is used to generate publication lists for departmental reviews.
-e, --exclude input filename. A file that contains titles of journals to exclude, one per line
-c, --conflicts output filename. Print the co-authors of all authors entered in -i or -n into this file
-h, --help prints help screen and exits

Author file format

Firstname\<tab\>LastName\<tab\>Initial

idoerg / paperchaser