Pub2Tools documentation

Pub2Tools is a Java command-line tool that looks through the scientific literature available in Europe PMC and constructs entry candidates for the bio.tools software registry from suitable publications. It automates a lot of the process needed for growing bio.tools, though results of the tool still need some manual curation before they are of satisfactory quality. Pub2Tools could be run at the beginning of each month to add hundreds of tools, databases and services published in bioinformatics and life sciences journals during the previous month.

Contents:

• What is Pub2Tools?
  • Overview
  • Dependencies
  • Caveats
  • Install
  • Quickstart
  • Repo
  • Support
  • License
• Usage manual
  • Setup commands
    • -copy-edam
    • -copy-idf
    • -get-biotools
    • -copy-biotools
    • -select-pub
    • -copy-pub
    • -init-db
    • -copy-db
  • Steps
    • -fetch-pub
    • -pass1
    • -fetch-web
    • -pass2
    • -map
    • -all
    • -resume
  • Parameters
  • Examples
    • Improving existing bio.tools entries
• Output
  • Output directory
    • pub2tools.log
    • EDAM.owl
    • tf.idf
    • tf.stemmed.idf
    • biotools.json
    • pub.txt
    • db.db
    • step.txt
    • web.txt
    • doc.txt
    • pass1.json
    • results.csv
    • diff.csv
    • new.json
    • map.txt
    • map/
    • map.json
    • to_biotools.json
  • results.csv columns
  • diff.csv columns
  • to_biotools.json attributes
  • Performance
• Ideas for future