pubmex 1.3

pu(b)mex: a scientific publication renamer

Pu(b)mex

pubmex.py is a script to get a fancy paper title based on given DOI or PMID.

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
    the title is ...  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

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

INSTALLATION

Python 3 is required.

git clone https://github.com/mmagnus/pubmex
pip install -e pubmex

Ubuntu (Debian-based system)

apt-get install xclip python-biopython pdftotext

.. clone & run it :-) Set PATHs to pubmex.py

MAC OSX

sudo port install poppler #pdftotext
sudo port install py-pip # 
sudo pip install biopython # or sudo port install biopython # (but it did't work for me)

.. clone & run it :-) Set PATHs to pubmex.py

EXAMPLES

Visit https://github.com/mmagnus/pubmex/wiki

Run a script with examples:

./examples-test.sh

BUGS

pubmex.py might have still problem if it has to parse title of authors with characters like ółą and so on.

HISTORY

1.3 Small fixes
1.2 Small fixes
1.1 simplify input, pubmex.py *.pdf
1.0: with recent bugfixes 2021
0.3: osx installation
0.2  Small changes