Pubmex

(tested on macOS and Linux)

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

Tricks

Copy paste the DOI into a filename and run pubmex.py:

$ pubmex.py 10.1038:s41587-022-01432-w.pdf
filename: .......... 10.1038:s41587-022-01432-w.pdf
mv  10.1038:s41587-022-01432-w.pdf -->Chowdhury.AlQuraishi-Single-sequence.protein.structure.prediction.using.language.model.deep.learning-NatBiotechnol-2022.pdf

or PMID:

   $ pubmex.py 35439059.pdf
   filename: .......... 35439059.pdf
   mv  35439059.pdf --> ./Vicens.Kieft-Thoughts.how.think.and.talk.about.RNA.structure-ProcNatlAcadSciUSA-2022.pdf

Install

pubmex.py is depended on:

• biopython (http://biopython.org/wiki/Biopython)
• pdftotext (http://linux.die.net/man/1/pdftotext)

you can install them with:

# Ubuntu (Debian-based system)
apt-get install xclip python-biopython pdftotext
# macOS
brew install poppler biopython # or "sudo port install poppler biopython"
# or biopython with conda, `conda install -c conda-forge biopython`

and then:

pip install pubmex

or get pubmex (the latest, version from this Github repository)

pip install -e git+http://github.com/mmagnus/pubmex.git#egg=pubmex

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! :-)

Alternatives

• https://github.com/MicheleCotrufo/pdf-renamer
• https://github.com/MicheleCotrufo/pdf2doi