Pu(b)mex

pubmex.py is a script to get a fancy paper title based on given DOI or PMID (can be also combined with macOS Finder)

Format of the title:

a first author . a last author - (title("dotted") or your customed title) . PMID . journal . year . pdf
e.g.
  Kelley.Scott.The.evolution.biology.shift.towards.engineering.prediction-generating.tools.away.traditional.research.practice.EMBORep.2008.pdf

Nowadays, it’s not a big issue, with all Mendeley and other tools, however...

I don’t want to put any PDF file collected on the way into my library, because then it gets super big (and then it’s hard to sync it for example with Dropbox). So now I can keep these PDF files into pdf-icebox and re-name them niecely automatically:

$ ls
Hnisz.Sharp.Phase.Separation.Model.Transcriptional.Control.Cell.2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

Usage:

$ pubmex.py sharp2017.pdf
Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf
mv sharp2017.pdf --> ./Sharp.Hockfield.Convergence.The.future.health.Science.2017.pdf

$ pubmex.py Query.Konarska.pdf
mv Query.Konarska.pdf --> ./Smith.Konarska."Nought.may.endure.but.mutability".spliceosome.dynamics.regulation.splicing.MolCell.2008.pdf
    
$ pubmex.py eabc9191.full.pdf
mv  eabc9191.full.pdf --> ./Balas.Johnson.Establishing.RNA-RNA.interactions.remodels.lncRNA.structure.promotes.PRC2.activity.SciAdv.2021.pdf

DEPENDENCIES

INSTALLATION

pip install pubmex
# Ubuntu (Debian-based system)
apt-get install xclip python-biopython pdftotext
# macOS
brew install poppler biopython # or "sudo port install poppler biopython"

HISTORY

  • 1.4 Add osx-automator
  • 1.3 Fixed #4 #5
  • 1.2 Fixed #2
  • 1.1 Simplify input, pubmex.py *.pdf
  • 1.0 With recent bugfixes 2021
  • 0.3 OSX installation
  • 0.2 Small changes
  • 0.1 Init version in 2010! :-)
GitHub - mmagnus/pubmex: get full paper names for downloaded publications automatically
get full paper names for downloaded publications automatically - GitHub - mmagnus/pubmex: get full paper names for downloaded publications automatically
GitHubmmagnus