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m4rx9 edited this page Oct 21, 2010 · 24 revisions
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PUbMEX.py – pronounced pumeks

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

Format of the title:
a first author(uppercase) . a last author(uppercase) – title(“dotted”) . PMID . year . journal . pdf

To manage your pubs you might take a look at http://www.mendeley.com/ and/or http://www.zotero.org/ and/or http://alternativeto.net/software/mendeley/

Download a package (with a PubmexWEB)

http://github.com/m4rx9/pubmex/archives/master

PubmexGUI (linux version)

Start:

python pubmex_gui.py
Your browser does not support the video element.

DEMO: http://dl.dropbox.com/u/472680/out-5.ogv

Type DOI or PMID and press the button :-)

Define your keywords – the filename will be replaced by them.

PubmexWeb

You might take a look at a web app of PubmexWeb http://maximus:9001/ (only for genesilico.pl :-( )

Your browser does not support the video element.

DEMO: http://dl.dropbox.com/u/472680/out-4.ogv

PubmexCMD

Your browser does not support the video element.

DEMO: http://dl.dropbox.com/u/472680/out-6.ogv

pubmex.py -p 20533529 -k 'MLH1,PMS2'
Kosinski.Plotz-MLH1.PMS2-20533529.HUM.MUTAT.2010.pdf

If you give a file it will try to detect a DOI inside the file

python pubmex.py -a -f demo/demo01.pdf 
DOI: 10.1038/nature07600
FILENAME: demo/demo01.pdf
demo/demo01.pdf -NOT→ demo/Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf
Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf

README

magnus@debian:~/workspace/pubmex$ python pubmex.py -h
magnus@maximus:~/papers/rna$ pubmex.py -h
Usage: pubmex.py [options] id

 examples: pubmex.py -p 17123955; pumex.py -p 10.1038/embor.2008.212;
pubmex.py -a -f file.pdf -r

Options:
  --version             show program's version number and exit
  -h, --help            show this help message and exit
  -p PMID_OR_DOI, --PMID_or_DOI=PMID_OR_DOI
                        pass PMID/DOI of the paper
  -f FILENAME, --filename=FILENAME
                        filename of a pdf
  -a, --automatic       try to get DOI automatically from a pdf
  -k KEYWORDS, --keywords=KEYWORDS
                        pass your keywords which makes a filename in a format
                        'RNA, structure'
  -r, --rename          rename files (only in a automatic mode)

# get a title based on PMID
python pubmex.py -p 20533529 
----------------------------------------
Kosinski.Plotz-Identification.of.Lynch.syndrome.mutations.in.the.MLH1-PMS2.interface.that.disturb.dimerization.and.mismatch.repair-20533529.HUM.MUTAT.2010.pdf

# get data based on PMID, change a title to keywords
'python pubmex.py -p 20533529 -k MLH1,PMS2'
----------------------------------------
Kosinski.Plotz-MLH1.PMS2-20533529.HUM.MUTAT.2010.pdf

# get data based on DOI
python pubmex.py -p 10.1038/embor.2008.212
----------------------------------------
Kelley.Scott-The.evolution.of.biology.A.shift.towards.the.engineering.of.prediction-generating.tools.and.away.from.traditional.research.practice-19008917.EMBO.REP.2008.pdf

# get data based on a given pdf file, show a new new, DO NOT rename
python pubmex.py -a -f demo/demo01.pdf
----------------------------------------
FILENAME: DOI: 10.1038/nature07600
demo/demo01.pdf -*NOT*-> demo/Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf
Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf

# get data based on a given pdf file, show a new new, DO rename
pubmex.py -a -f demo/demo01.pdf -r
----------------------------------------
FILENAME: DOI: 10.1038/nature07600
demo/demo01.pdf -*DO*-> demo/Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf
Jovanovic-Talisman.Chait-Artificial.nanopores.that.mimic.the.transport.selectivity.of.the.nuclear.pore.complex-19098896.NATURE.2009.pdf

PROBLEMS
If you get

IOError: [Errno socket error] (-2, ‘Name or service not known’)
just re-run the script.

Wanna get to know more see README file.