This script supports generate a Conflict of Interest/Collaborating Authors file from a PubMed query.
Write a Collaborating Authors table suitable for USDA/NSF COA/COI files. Note this will not cleanup issues where authors do or don't have middle initials included so the list may have some redundancies. This should be easy to cleanup manually once you have the list.
The prefix "A:" is following the NSF COA policy - if you need to simplify this in USDA format should be easy enough to do manually. Arguably it should do better to pull out institutional affiliations to separate department name out, but this seems a bit hard to do well right now so it is just the whole institutional address from the publication.
It is best to replace yourname@email.com with your actual email address!
Run a search and print out the record IDs for the US Biologist Tyrone B Hayes, write to the file coi.tsv.
./pubmed_authors_to_COA.py -v -q '(Hayes TB OR Hayes Tyrone)' -e yourname@email.com
Generate report of co-authors in publications since 2017 into file coi.tsv for the US Neuroscientist Erich Jarvis. No printing of record numbers while running (quiet mode).
./pubmed_authors_to_COA.py -q '(Jarvis Erich or Jarvis ED) AND (("2017/01/01"[Date - Publication] : "3000"[Date - Publication]))' -e yourname@email.com
Generate report in file Blackwell_M_co_authors.tsv for the US Mycologist Meredith Blackwell.
./pubmed_authors_to_COA.py --query 'Blackwell Meredith' -o Blackwell_M_co_authors.tsv -e yourname@email.com
Generate a report for only the first 2 publication records into file Treseder_authors.tsv for the US Ecologist Kathleen Treseder
./pubmed_authors_to_COA.py --query 'Treseder KK' -max 2 -o Treseder_authors.tsv -e yourname@email.com
usage: pubmed_authors_to_COA.py [-h] [-v] [--debug] -e EMAIL -q QUERY [-m MAX]
[-o OUT]
optional arguments:
-h, --help show this help message and exit
-v, --verbose Print out Verbose processing
--debug Debug only printing one record
-e EMAIL, --email EMAIL
Email address for Entrez query
-q QUERY, --query QUERY
Pubmed Query
-m MAX, --max MAX Maximum number of records to retrieve
-o OUT, --out OUT Output file name