biblioplast

Utility scripts to pull PubMed info as CSV or JSON

Both scrips read PMIDs from stdin (1 per line) and query Pubmed. Currently the JSON output is the full record, while the CSV output is: PMID, Title, Abstract

Useful bash:

Get PMID column: awk -F"," '{print $1}' file.csv Check errors: cat output.csv | grep "Error" | awk -F"," '{print $1}' | python PMIDtoJSON.py | less